HELP–how to use custom php?

I just upgraded to CatchBox 3.9 and the templates directory has disappeared. I was using it for a couple of custom php files for a critical plugin which is vital to our site. Please tell me where to store the php so that customization works.

I understand that child themes is the way to go but frankly that is beyond the pay grade of anyone working with our non-profit. In the past it has not been a problem with updating CatchBox and quickly reinstalling the php in the templates folder. We want to continue doing that.

Thanks