Modswapper takes it's options from the gamefile's so in your CTP folder\ctp2_data you should find a file called CRA_gamefile.txt. If that's not there, you extracted into the wrong folder...
Anyway - what kind of zip programm do you use?
Theoretically the whole info on the file placement in folders is saved in there and when you extract the zip into the main ctp2 directory it should work out fine.
Try this - extract the zip to your C drive - do you get a folder called ctp2_data? If so, copy that folder into the main Ctp2 directory where (as maq pointed out) should also be the modswap.exe. You'll be prompted for a permission to overwrite, say yes and everything should work.
Now if it doesn't - tell me exactly at which stage this is failing. You could also send me a screen print (push Prt Sc on the keyboard insert into MicrosoftPhotoEditor and save as jpg.) of the explorer showing the insides of your main ctp2 folder and your ctp2_data folder to
mapfi@hotmail.com.