Ordered all sample set of everything.
Good move.
Do you know which ones are most popular for the molds?
Popularity really varies, since each mold has different sound/feel/performance characteristics (and different people prefer different characteristics). The A-mold is CPC's biggest seller. A lot of people prefer the diasqr mold. YMMV.
and color for the tournament chips?
The 'standard' colors for tournament chips are 5-red, 25-green, 100-black, 500-purple, 1000-yellow/orange, and 5000-gray/pink.
I kinda have an idea of the colors I want for the cash game chips. (White for 1s, Red for 5s, Green for 25s, black for 100s and maybe something for a few 500s).
Those are fairly common colors for those denominations.
Normally when we place an order, there is an option for both edge spots and mold?
Check out the Chip Design Tool - there is a link at the top of this page.
How do you choose how many edge spots and what not?
After playing around in the Chip Design Tool for awhile, start a 'help me design my set' thread, and you'll get plenty of experienced advice.
What about other customizations like color in the center or more than 1 color like half/half on some chip sets I see?
Most people utilize a professional chip designer/artist to help with their custom artwork. There a several great ones who hang out here at PCF.