Though COTS gearboxes are recommended for teams who have not designed or prototyped custom gearboxes in the offseason, there are plenty of resources to help teams design their first custom gearbox, if you would like to give it a try.
To determine PD, OD, and center to center spacing of a gear, WCP has a neat feature on this page:
http://wcproducts.net/how-to-gears/
To determine your desired gear ratio, use JVN's mechanical design calculator:
http://www.chiefdelphi.com/media/papers/2059
In order to figure out mounting holes for a shaft encoder, check out
http://www.chiefdelphi.com/media/papers/2681
Many of these resources make it easy to design a custom gearbox in CAD, but you do have to know what type of speed and ratios you want.