No need to activate the alternative flotilla's mod if you don't want to. The merged campaign lets you start from any of the standard GWX ports without having to load either the Black Sea or Indian Ocean Campaign files.
You will notice slightly longer load times due to the fact that the merged campaign is a bit bigger than the 3 separate campaign files.
It is always a good idea to return to port before changing anything to do with campaign files.
Gute Jagd!
