Alright... even I'm getting confused...
Install ASE, start it...
answer all the wizards questions....
now, go view -> options, games tab
Find GTA3:MTA under the 'Not installed' thing.
Select it, and hit the 'browse...' button.
find mta.exe (should be in C:\Program Files\Rockstar Games\GTA III\mta.exe)
hit ok.
now select GTA3:MTA from the list on the left hand side, click refresh, and that should do it.