Hello, I don't have any experience at all with the backflip, but I know that for the evo, we have an app called RomManager which does all the work. It'll download and flash the roms for you. Unfortunately, it has been widely shunned by the root community there for various reasons, usually regarding stability.

You would be able to possibly use wireless ADB to send the nandroids that you'll eventually (probably) make to a secure backup place (computer).

epsi:
here is the link to the backflip root forum, I'm sure they'll be able to get you all sorted out far better than myself.
http://androidforums.com/backflip-all-things-root/

EDIT: So I'm moving this thread to the backflip root forum. And questions or concerns feel free to PM me.

 

I'm sure the phone has some place where it downloads files, and if you can locate that you should be fine.

 

My usb connection doesn't work, so anytime I want to put a new ROM on my phone I use Airdroid which can send files to your phone from your PC using a wifi connection. It sends them to the root of your sd card which is quite handy as you don't have to sarch around for the file you sent and move it there manually. It is also good for many other things, such as sending texts from your browser, managing files, and has an app manager (to name a few.)