I have one character with three different playthroughs on it, so does anybody have an idea which playthrough ME2 will pull my save froms to find out what i did in it?

Im guessing the last playthrough you did with it.

They might allow to choose which save you which to load from?

You will get a list of saves to pick from. I'm not 100% sure if you will be able to pick the same character multiple times if you did multiple playthroughs but different characters, definitely.

If it dosent let you choose then you could just copy the saves you dont want to use off to a memory card/diffrent folder.

Whenever you finish the final boss, the game makes a separate "final" save away from all other saves (this is what you see whenever you make a new game+). Presumably these saves are what will be used in the second game.