I am thinking the easiest way to make multiple mods sometimes before the next millenium is by replacing the S14 teams and keeping the updated version of MUP09.
So it works as MUP09 with it's updated menu graphics plus all the default euro teams, then i will use the Super 14 teams to add ANZ Cup, Currie Cup and an original patch, so there will be four seperate patches, just with the Super14 teams replaced each time. When the teams need updating, you can then just add the new files into each directory.