How to plan overnight train transportation

Your question is confusing. Do you mean you have 6 days to sightsee Amsterdam and Venice AND travel from one city to the next? If so, I would fly that route. You could do trains in many configurations but you're going to spend a lot of time in transit (likely between 16 and 20 hours) and change trains at least twice.

If you have 6 days in transit and then also have 3 days in Amsterdam and 3 days in Venice, well then you'd be fine taking the train with a couple of city stops in between. Those possibilities are endless - you'd have to do some research to see what interests you. Munich would be a good city to consider as a stopover point.

We just have to arrive in Venice. We wanted to plan two days one night in Amsterdam ,two days in Paris one in Switzerland and maybe a stop in Milan.

I'm sensing that your timing is kind of rushed. How many nights total do you have in Europe? Is this your first trip? Without a doubt, you are not allocating enough time in Amsterdam or Paris. If you're only staying one or two nights in these far-flung places, you will see very little at all on your trip. At a bare minimum, most cities are worth a 3 night stop and even at that pace, you're going to just see the basics for a city.

There used to be City NightLine trains from Amsterdam to Munich and from Munich over Brenner Pass to Venice, but those have been discontinued. There is still an EN night train from Munich to Venice through Salzburg and Villach. So, you could take a high-speed daytime train from Amsterdam to Munich and pick up the night train to Venice.

You could also take day-time trains from Amsterdam to Munich, spend some time in Munich, then take another day-time train over Brenner Pass to Venice.

If you want to go via Paris and Switerland, you've got the route right. Go to Paris for a night of two, then to the Berner Oberland, then to Italy via Brig, possible overnighting in or near Milan.

I have to agree with Valerie. You're really pushing it timewise.

Look up the scedules on the Bahn website.

There's no need for an overnight train from Amsterdam to Paris. Thalys trains make the trip in 3 to 4 hours. From Paris to Venice, there is a 14 hour EuroNight train, but you might like to do it during the day for the scenery.

Overnight trains are a dying breed and for good reason. They are horrible and flying is much cheaper. What do you mean by Eurorail?

I'd suggest spending one more night in A'dam and then taking the train to Paris and then flying from Paris to Venice.

Easy jet has flights for as low as 43 EUR from Paris to Venice that take 1 hour and 40 minutes. Add 3 hours time to get to the airport and 2 hours from landing to get to your hostel in Venice.
There is a night train from Paris to Venice, taking 14 hours and a berth in a 6-person couchette costs 35 EUR.
Buy direct at: https://www.thello.com/index.html?iLangID=3
Do not use Eurorail (Rail Europe actually). They are just an overpriced travel agency.

Elaine, you wrote "on the Eurorail". I hope you are not making the mistake of assuming there is a company called Eurorail running trains, there is no such thing. "Eurail" is the brand name of a rail pass sold mainly in North America.
Trains are owned and operated by many different companies.Mostly national companies (DB in Germany, SNCF in France, Trenitalia in Italy etc.), plus many local companies and some independent competitors and joint operations for international trains.

As the others have said, there are very few overnight sleeper trains remaining.
See this page for more info: http://www.seat61.com/sleepers.htm
And the rest of the website for lots of independent info about travelling by train.

6 days = 5 nights Amsterdam to Venice. That only gives you time for two stops, 2+3 nights (Golden rule: No one night stands).
I would suggest 3 nights Paris + 2 nights Berner Oberland.
Thalys High Speed train Amsterdam to Paris, TGV high speed train + local connections Paris to Berner Oberland, Train from there to Venice. None of those legs have overnight trains.

Elaine, our host here, Rick, is famous for his train travel advice, which is free content on the main part of this site. I commend it to you for basic research. I personally would not go so far in six days.

Keep in mind the luggage size and weight limitations on bargain air lines, although that was a good suggestion if you insist on this once-in-a-lifetime-Europe-assumption itinerary. I also agree that overnight trains to save the money of impoverished backpacking students have gone out of fashion. Some people worry about overnight crime on trains, but I don't know if those are real stories or urban legends!

You have left your home state and country off your profile, and the cryptic note about six days prevents us from giving you our best possible advice.

I like to travel slow and my temptation is to tell you to see only Amsterdam and Venice. Fly between them. If you must see more places, add Paris. Paris is a short high-speed train ride from Amsterdam. From Paris you can take a sleeper train to Venice. As you may have noticed, sleeper trains get mixed reviews. Our family loves them. They take longer, but the longer occurs while we sleep. When you arrive you are where you want to be and not at the airport, a time and cost savings. There is no security check.

But they are not for everyone. They do stop off and on all night. Your compartment mates may get on very late. The beds are narrow and hard. The toilet is outside the room. There is no shower in the four and six berth compartments. You will share the compartment with strangers who may or may not speak your language. We have had mostly happy cultural experiences with that. That worst has been passengers wishing to be left alone--not a real problem. It is more like camping than staying in hotel. We bring a washcloth and hand towel each so we can take a quick continental "bath" in the morning. See here for instructions on purchasing tickets for and taking the sleeper. http://www.seat61.com/international-trains/trains-from-Paris.htm#Paris-Italy

We have taken this particular sleeper as far as Milan.

one night is no days but two fragments of days and remember hotels require check ins late and check outs early. It takes two nights to get a full day in place and 3 to get two full days. Two days for Paris (especially if that means one night) is not worth the bother. When you rush like this you end up spending most of your time on logistics and very little time on actually seeing a place and doing things there. It can work in a small town, the ratio of hassle and logistics to payoff in a big city like Paris is way out of whack.

Your compartment mates may get on very late. The beds are narrow and
hard. The toilet is outside the room

This is only true for the shared couchette cars. One can also pay a bit more for the private sleepers, which have bigger beds, sitting area, and sometimes an en-suite bathroom with shower.
The CNL deluxe sleepers also have large windows which are positioned so you can see the scenery go by while lying in bed in your underwear.

Night trains are awesome!!!!

CNL will cease to exist in about 2 weeks.

This is your only reasonable opportunity to use a night train, Paris to Venice, and you'll have to skip Switzerland, which you really don't have time for anyway.
http://www.seat61.com/thello-train-from-paris-to-italy.htm

CNL will cease to exist in about 2 weeks.

From the Seat 61 site:
Update 2016: Unfortunately, Deutsche Bahn has announced that it will discontinue all its City Night Line trains from the timetable change in December 2016. The good news is that Austrian Railways ÖBB will take over some of these services, as shown below, under the new brand name NightJet.

@ elaine...Keep in mind that there is a basic distinction here if you are planning on taking the night train option, which I would. CNL is going out, as correctly pointed out, but night service will still continue to be in operation since it is done by EN. There are numerous night train routes done by EN. There was never any question that once CNL was discontinued, as expected by announcements from DB, that would mean the end of all night service. Night service was not ending, only CNL was.

If you want to squeeze out an extra day, take the night train route where that is possible, also depending on how you tailor your train travel routes.