If you have set up an SVN server, you should use that. Work on the fork, commit changes you make. Keep your original GZDoom folder in pristine state, that way you can quickly make comparison tests when you discover a bug.
With TortoiseSVN, merging changes is easy. Just show the GZDoom log, select the revisions not backported yet, and then right-click->merge revisions to:
Navigate to select your fork folder, and there you go.
If there are any conflicts, you can edit them during the change.
Once it's finished, commit.