Polaris, I almost got uber pissed at you...
For one thing: my motherboard won't boot with the USB drive in... I thought the utility killed my mobo
The utility might damage your USB drive, but that is extremely doubtful. The only way you could have damaged your motherboard doing this would be to force the USB drive in the wrong way. Don't be silly.
You did exactly what you needed to resolve the problem. You knew when a removable drive doesn't boot properly, that something isn't set up correctly so you removed the drive. Exactly like having a non-bootable floppy disk in your computer. Your computer won't boot in that situation either correct?
For another: when I formatted, I only had a few KB left of my flash drive...
It does that.
luckily I was able to reformat the drive back to stock... I should just use a real floppy drive...
Luck had nothing to do with it, the software formatted your drive that way. Formatting it back fixes the problem.
Obviously this isn't the best way to do this since you both had problems.
Here is where I learned how to make USB boot disks. The way I showed you was the one I thought was the easiest, maybe it would be best if you looked through the list and found one that works for you.