I'm building my first homebrew subclass and one of the subclass feats adds 2d6 damage to spell attacks at lvl 5, 3d6 at lvl 9, and 4d6 at lvl 15. I found the upscaling tab in the class feats and added the separate upscales for each level but it isn't automatically adding the bonus damage when the spell (like firebolt) damage is rolled during testing. I don't really want to have to do it manually unless I have too. Do I have to specify what spells to add the bonus too? Any advise is appreciated. Thanks.

There is no way for a class feature to automatically add damage to spells. You will have to roll it separately.

Bummer 😞 Thanks for your insight. 

Also, since you say it's your first I feel obligated to point out that your feature seems way overpowered. No subclass in the game adds that much damage unless it only applies once per day or something.