The Rivals for Catan - Theme Game Draw Stacks
Does this mean, each user selects a
  stack, looks at all the cards in the
  stack and selects the 3 they want
  start with? And then returns the stack
  without reshuffling?


Yes, that's how I always play it.  I don't see any other way to interpret that rule.


  How do the Theme Set draw stacks work?
  There is nothing in the manual about
  how players draw from them. Do players
  have the option of drawing from them
  after their first turn?


The rules for drawing cards on p10 state, when drawing cards:


  ... randomly draw cards from the tops of the draw stacks.


Although it's not entirely clear from this rule, I think you can always choose which stack to draw from.
Also when exchanging cards:


  Draw the top card from a draw stack of your choice,


or


  Choose a draw stack and look at all of its cards.  Then take 1 card of your choice from that stack.


None of these is restricted to only the basic set stacks, so you can draw from or search theme set stacks too.  The only restriction is at the start of the game, when you choose your three starting cards from a basic set draw stack.