Your hardware is good enough to make 1:1 copies with CloneCD.

You should be able to back up both games by copying them the same way as u copied Dungeon Siege.

The cd backup patch is unnecessary if u can do a 1:1 copy, but the patch is probably a no-cd.

You can update a game that has been patched with a no-cd crack, as long as you replace the file which you originally replaced when you used the no-cd patch, (to do this you would need to keep a backup of the original replaced *.exe file that u replaced when u overwrote it with the no-cd file, or you could just not use the no-cd crack untill you've got the game updated enough.) Also you'd need to have the right no-cd crack to corespond to the version of the game, probably depending on what you've patched it to.

I usually use cracks for backing up games. Unless i can't find a crack, then a make a 1:1 copy. The reason for this is that there's a better chance it'll work if you use a crack.

Sometimes you might come across a strange game with a few different types of protections you might have trouble with (i had a lot of trouble with Operation Flashpoint Gold Update and Emperor battle for dune, but i got them done, with some help from people here

I have GTA3 and Medal of Honor, and i copied them both with 'fixed .exe's' and 'no-cd' cracks (btw a fixed exe, is pretty much the same as a no-cd, but a 'fixed exe' crack, still makes you need the cd to play it.) But you could probably copy them both with Clone CD