Every modification I made in vB3 was a result of hit and trial.
Things became a lot easy when they added the advertising module in vB4 that enabled me to put in my ad codes and other scripts easily on the forum without modifying the core files.
I expect to see something like this in XF too.
An add-on that I found for vB4 has also become very useful for me... It basically let you add your own CSS code in the backend. This CSS code is processed at the end of the theme code so your own properties override all the previous ones.
The benefit is that you can make small modifications to the forum without messing around with the default theme and it is all available at a unified place.
I use it to change the font size of the post content and some other minor changes.
This suggestion is largely a result of this thread: