hey there
took me a while to get my head around it aswell
firstly if its already flashed there is no need to reconnect it to a pc to back up the games aslong as you buy the specific drive that can backup the games.
its called the Samsung SH-D162C (thats what i have) THIS IS A PC DRIVE NOT A REPLACEMENT 360 DRIVE!
that needs to have the "kreon" firmware installed on it, for it to be able to read and copy the 360 games.
You can find these cheap on ebay, picked mine up for about £15
Next step is preferance as to what program to use, but i use Xbox Backup Creator to copy and burn my backups. (obtained from usual source)
That program has an easy user interface and ive had no problems in using at all.
Also when burning use Verbatims, again search on ebay for "verbatim 360" or something like that
They are the best media to use and i have had 100% successful burns using the combo that i have described.
The only difference is that i have a sony dual layer burner, but seeing as most users on here use the pioneer you shouldnt have any problems
Think that covers most things
Feel free to ask more questions