Ok well if you have a mod chip, my method... is to just use DVD Decrypter. Copy the disc. Presto! Mind you there are SOME cd-only games that will be libcrypted (although I think that was really only PSX games, but I can't be certain). So DVD Decrypter for DVD based games, CloneCD for CD based games.
As for dual-layer, well it's really only GT4 (and a couple imports) and there are instructions on the PS2-only sites for making a working backup on two discs (or one dual-layer) of GT4.