Making sure settings are correct

[Creeper]

Alright im not compltely new to psx backups but i am new to using the patches for protected games. such as the one i am about to attempt to back up.. Resident Evil Survivor.. i know its protected and already have the patch as well as ppf-omatic 3.0
since i do need to apply the patch i plan on using cdrwin3.8 with its settings for normal reading of roms. it is going to create it into bin/cue for me like neother time... now to apply the patch i open up the gui for ppfomat.
heres were im alittle confused. when u go to set the directory for the image file mine says locate iso.. does this mean my file has to be in iso format to apple the patch. for screen shots that i have seen on the gui for ppfomat shows locate bin file?
pretty much my question is does the ppfomat patch have to be in bin or iso format to apple the patch if so then what program should i used to make an iso. i dont think clone cd is compate with my writer...