The Fit advisor within BikeCAD Pro can help determine an appropriate Rider compartment measurement. Although, I should warn that the Fit advisor is mostly intended for Fit specialists who wish to apply their own fitting philosophies to a bike. This is why the Fit advisor can be customized as described at: bikecad.ca/customizing_fit_advisor.

As for chain stay and seat stay lengths, the auxiliary views available within BikeCAD Pro can help to determine what stay lengths might be feasible if your goal is to make them as short as possible while still allowing for tire, chainring and possibly fender clearance. Meanwhile, be aware that the objective should not always be to have the shortest possible chain stay length. If you're building a touring bike, you'll want longer chain stays to make room for panniers. If you're building for a taller rider and need to stretch out the front end of the bike, you may need to lengthen the stays as well just to keep the weight distributed appropriately between the two wheels.