All the file does is patch your gta-sa.exe file, so just make a backup of your original in case something goes wrong. That's the only file it changes as far as I know.
It is a downgrade patch, so you'll lose any bug fixes from 2.0 and I'm not sure if your savegames will work (they should).
You should have the latest version of DirectX (9.0c).
Confirm to us that you have a clean install of San Andreas with no other mods installed, and try deleting gta_sa.set file and restarting the game (your settings will be reset).
Does it say Version 2.0 on your retail box? If not, you should have 1.0.
Do you have ANY other mods installed for San Andreas besides MTA? MTA only works on a clean install of the game.
Try deleting your gta_sa.set file in My Documents\GTA SA User Files and restarting the game.
Though they merge, car modders often also do it be annoying.
Actually, I don't see any other purpose in it. If your idea of fun is flying through the city at 999 MPH, why do it online?
That may be true to some extent, but remember there are still millions of potential fans who have not yet even heard of MTA. Besides, I think MTA:SA will bring a new experience to San Andreas that will give it good replay value.