Life is easiest if you put both sorts of components on the same side of the board - putting SMD components on the track side the board means that they have to be glued down before the board can be reflow soldered
- it isn't a big deal, but ti is an extra operation.
Solder-paste masks work the same way as every other mask - you don't need special alignment masks (at least not anywhere I've worked).
The printed circuit board house that makes your boards should be able to tell you all about this sort of stuff.
---------- Bill Sloman, Nijmegen