norse
You'd do better to post this in the GOTM forum, or PM cracker (the GOTM admin) with any issues.
The short answer to the first question is "it depends". PTW GOTM generally adds files (as new scenarios) but does not change existing stuff. Civ1.29f GOTM does need to change stuff to keep the two versions similar, but the changes are relatively minor and quite well explained, and the staff will help you if you get confused, especially if you
PM them - open discussions about ongoing games are heavily frowned upon.
And, yes, you need the save file to start with - which you can download from a location which is revealed to you during the installation process of any mods required (to make sure you do install stuff right, first).
I suggest you go to the main CivFanatics page and take a look at the GOTM pages which explain most of this, take a look at the set up for one of the games (which will hopefully explain more) then either PM one of the staff or, if a general question, ask it in the GOTM forum where the GOTMers can more easily spot it and help you.
While the setup may look daunting it's an excellent experience and well worth the effort IMHO. Good luck
