Paris' Museum Pass - Transportation

You'll take the Metro from your hotel to the Louvre or Orsay, whichever you want to go to first. You'll walk from the Orsay to the Louvre, or vice versa. The Louvre is just north of the river and the Orsay is practically across the river from the Louvre.
To Versailles is different, you'll take the RER-C train to Versailles, after using the Metro to get to a station where you can connect to the RER train. You'll have to do a little research to find out how the Metro and RER work.

Realistically, you won't want to try to see all 3 in one day. Versailles is 35 minutes southwest of Paris and the lines both outside and inside are long, and it's huge. Most people seem to take most of the day to see Versailles.

The Louvre is one of the largest museums in the world, so you won't "see" it in a few hours, that would take days, months, or years. You'll do some research and pick a couple of sections of the Louvre that are of most interest to you, and then you can spend 2 to 4 hours in the Louvre.
The Orsay is much smaller than the Louvre, you can actually see most of the Orsay is half a day.
So you could do Versailles in one day and the Louvre and Orsay in another day.

I've seen both museums many times but on last month's trip to Paris we spent all day at the Louvre, eating lunch and dinner at the food venues there. And then on another day spend 6 hours and lunch at the Orsay and then returned another evening when they are open late.

But I'm an art nut and love the Orsay Cafe. For you, you can still see some of both museums in the time I've described above.

Are you planning just a 2 day Paris Museum Pass - it also comes as 4 and 6 day.

From your hotel Metro line 13 (aqua) from Gaite to Invalides.
Its a short walk along Seine to Orsay, then across the river and through the Tuileries to the Louvre.
Metro line 4 (purple) from Chatelet to Montparnase returning to your hotel.

From your hotel Metro line 13 (aqua) from Gaite to Invalides, then RER C (yellow) to Versailles.
Reverse journey to return.

Rachel,

The Metro is about the easiest way to get anywhere in Paris. Many people buy a Carnet of 10 tickets and just use them as needed. There's also the RER which is useful on some routes.

You may find it helpful to have a look at the excellent *Paris By Train website. I'd also recommend packing along one of the guidebooks (ie: Pocket Paris) as that also has good information on transit.

Carnet tickets are the way to go within central Paris, but to get to Versailles by RER you will have to buy a specific ticket for that journey.

Personally, I wouldn't attempt to see more than one of those locations in a single day.

There are a couple of days that the Louvre is open until 9:45pm (Wednesday & Friday) so if you are in Paris on either of those days, you could easily go to the Orsay & the Louvre on the same day. You'll want to figure out what you want to see in the Louvre since its huge and you could spend days in there, literally. Versailles is at least a half day if not a full day by itself. Enjoy!

Do you have a guidebook? Any of them will have the answer to this question, as well as lots of other useful information that you didn't even think to ask about, but will be glad to have. I think Rick's are particularly good for first timers, as they really give lots of detail on things like using the Metro, what to expect in a restaurant, etc. For a short trip, you can make do with the Pocket Paris guide; for a longer one, get the regular Paris guide.