Ball screw pitch question please

Hello all,I have been lurking for a while and now I have a question
that I hope someone has a answer to my concern.I have been building a
bench top CNC from whatever I can machine plus parts from e-bay and
parts I find.Basic concept of what I have is Thomson rails and ball
screw on Z axis with .2 pitch per rev,and on X&Y,the same Thomson
rails,but with .5 pitch per rev.How will the controller(which I don't
have yet,nor have any idea of what to choose including motors)
understand the pitch differance's so that it can operate properly.I'm
still trying to put a spindle together at the moment,so all I have
now is manual axies until I select my servo's or steppers.It's
roughly 16" X,8" Y,9" Z travel machine.I hope I haven't shot myself
in the foot by not getting common pitch screws:(

Regards,Steve