The chain stay bridge is controlled at the bottom of the chain stay dialog box. Note that chain stay bridges will only be available for non-wishbone stays. One of the inputs allows you to enter the distance from the rear axle to the center of the bridge. If the bridge has a brake hole, then the bridge is located by the distance from the rear axle to the outer face of the brake hole, not the center of the bridge. Seat stay bridges are similarly controlled through input fields at the bottom of the seat stay dialog box.

Evan, I noticed that you have just registered an account on the BikeCAD.ca website. Since you purchased BikeCAD Pro from the old website, your new account did not initially identify you as a customer. However, I have manually changed your status to BikeCAD Pro owner and have granted you access to download the latest version of BikeCAD Pro. If you don't already have it, you can download it as per the instructions here. I invite all other BikeCAD customers who do not yet have accounts on the BikeCAD.ca site to register for an account today. Let me know when you've done so and I will give you access to download the latest version of BikeCAD Pro. I also recommend filling out your profile to promote your business as described here.