LC is just a reskinned VC, so it's all the same tools *imgtool works for gta III, VC and San Andreas as well*
As for the files, do you mean you can't figure out what collisions you need to replace? If so, there are 2 directories for the .col files and depending on what version of the LC mod you have, it could be reading from either one so replace both just to be sure.
Inside the gta3.img you'll find different .col files that represent sections of the map, I believe by memory that the updated files just replace entire corrasponding .col file *ones with the same name* if the new ones are too big to replace then delete the old one and import the new one, I'd suggest either backing up the individual files or the entire gta3.img/gta3.dir just in case something goes wrong.
The other locations are in DATA>MAPS>(map section) each folder for the different map parts have a .col in there that you'll need to back up and replace
