How do you determine which Dominion sets to play with?
There is no general way to pick the sets besides picking ones that you like.

I generally restrict myself to 2-4 sets of cards because I like to play with at least 2-3 cards from each set I am playing with (this is especially true if playing with alchemy).

In my opinion, the only 2 sets that I have found to clash, and its not even that bad when they do, are dark ages and hinterlands.

You might also consider reading this question: Does mixing Dominion expansions lessen the power of card combinations in random kingdom setups?