I personally do all my flashes via Clockworkmod. I started out doing them in Rom Manager, but for some reason I was getting a lot of things forcing closed when I loaded Roms this way. I'm not saying this to try to scare you, it was just my experience and with that being said, more people have had good luck than bad with Rom Manager. When you want to flash something you can either download it strait to your phone or you can use your computer. I prefer the computer. Then place the .zip file on the root of your SD card. Since I do everything via Clockworkmod, I then boot into recovery, and then do a back up. I then scroll down to install zip from SD card, find the zip file I want to flash (another word for install) and let the phone do its thing. Remember, as long as you can boot into recovery, you can fix almost everything.