Ciao hotstuffjsn,
I am exactly in the same situation as you are and it is no problem.
Yes, you can rename everything so that you have two complete sets - one
for the GOTM and the other for the normal play - as per previous suggestion,
or you can keep everything together (my choice).
In my case it is typically a matter of swapping 2-3 files. Usually I play the GOTM
at the beginning of the month, I submit the GOTM, then I swap the file and play
a vanilla game for the rest of the month.
Ciao,
giama remil (playing Civ from Milano, Italy)