For cd based games use CloneCd. If your burner is DAO 96 compatible no patching is necessary. You can see if your burner is DAO 96 compatible
here For dvd based games PrimoDvd works best. No patching at all is necessary for dvd games. Check out
http://www.psxcopyworld.co.uk/ for the CloneCd and PrimoDvd copy tutorials. The site is currently down but should be back up soon. As far as using you AR2 to boot, try the various methods listed in the sticky Factoids: Ps2 Boot Procedures For All Mod Chips!