milan to lake como to cinque terre back to milan

• Yes, Milan - Lake Como - Cinque Terre - Milan sounds reasonable. "I am for some reason having so much trouble planning my latest italy trip" - You don't say what your problems/troubles are. If you specify, people can help.
• Lake Como is a big lake, with multiple arms (shaped like an upside-down Y), and many towns along all sides of the lake. You need to decide where on Lake Como before you can work out how to get there (some combination of rail, bus, boat).
• "then a day spent on the bernina express" "Is it wise to take bernina express from lake como?" The Bernina rail line does not run from Lake Como. It runs from Tirano (north-East of Lake Como), north, over the Bernina Pass to St Moritz and Chur. You would first have to get from wherever you are on Lake Como to Tirano, which would take a number of hours, before you even got on board. And you would need to repeat the trip back again via Tirano if you wanted to return the same night. It would be a very long day, if practical at all.
• To get from anywhere on Lake Como to the Cinque Terre you will need to go back via Milan.
• The Cinque Terre is, as the name implies, a region of 5 towns (Monterosso al Mare, Vernazza, Corniglia, Manarola, and Riomaggiore). You would have to decide which one you want to stay in before making detailed plans. All 5 are linked by a rail line that starts at Genoa. You would take a train: Milan - Genoa - town of your choice.

There are also direct intercity trains from Milano Centrale to Monterosso, the biggest of the 5 villages.

ok, so for bernina express, that is not a day thing? I was thinking of staying in Varenna for the lake region for two or three days and taking bernina from tirano to st moritz. I wouldn't mind spending a night there but I thought of the rail line something as a hop on hop off type of thing but I'm seeing that it's not... its more of a bring your luggage and at least spend one night? In that case we may not have enough time to come back through milan to cinque terre. If I spent the night in St moritz off the bernini express, should i just shoot down to verona after that? What would you suggest? We are totally open to parts of Northern Italy, preferably where there are vineyards. I think the most important aspect at this point would be linking lake region to bernini to another point in northern italy. We are spending two and a half days in lake region potentially taking bernini express on a thursday and needing to be back in milan for sunday evening. We've done Venice so don;t need to go back there again.

Tiffany, the Bernina line is a rail route OVER the Alps. It is scenic because it is the only route that goes over the Alps instead of going through long tunnels. It is a rail line from A to B with one train in each direction per hour, not a circular trip, the only way back is the way you came, or continue into Switzerland. It is best incorporated into a trip as a method of getting between Italy and Switzerland.

Some sample times:

• First train of the day from Varenna-Esino to Tirano (and if you are not staying in Varenna you need to get there first): depart 07:24 arrive 08:52 (Italian train times from http://www.trenitalia.com/tcom-en )
• Tirano to St Moritz: depart 09:00 arrive 11:11 (Swiss train times from https://www.sbb.ch/en ). But that is a short transfer as it is two separate stations, safer: 09:41 arrive 12:11
• Back to Tirano: 12:38 arrive 15:00
• Back to Varenna: 15:08 arrive 16:36

But, if you wanted to continue to Cinque Terre (for example Monterosso):

• 15:08 depart Tirano, 17:40 arrive Milano Centrale (same train as above, just don't get off at Varenna)
• 18:05 depart Milano Centrale, 21:03 arrive Monterosso

That is a very long day, the majority of it sitting in trains. Your choice.