Questions Regarding un official downloads

[Kuriltai]

I see what you mean.I am suprised nobody else has climbed in here.
However,I think I am still on the right track.Anyone's scenario pack should have new names for any OOB and scn files (map files should always be the same,except in the official update's I think) so no overwriting worries there.The only files I would worry about are bmps, sound,weather and in my case the 2dsymbols.
At any rate,making a new folder(in your case for every different download)gives you the opportunity to look before overwrite.
This is my solution.There are probably better.

Kuriltai