I'm trying to learn them both, but I'm leaning towards using TunerPro as my go-go tool once I really understand how to do all this correctly, mostly because of the checksum plugin.
I'm working on learning how to use IDA in order to define my file as no-one here seems to have a definition for it, I think it's going to take me about five years. We'll see which comes first, my MBA, or my tuned file.