Cant edit my post for some reason so will just answer my own question incase this comes up in someone else's search.
Step 1. create a single bin/cue using daemon tools lite and imgburn
Step 2. patch the bin
Step 3. replace the cue file with the correct one from the patch folder
Step 4. most...
Currently trying to get TR2 going on a CFW PS3. Regarding the patcher, TR2 is a multi track game, do you patch each bin file? Or should I create a single bin/cue and then patch?