Right now I'm using Wubi to install Xubuntu 12.04 on my 8GB flash drive, and I'd just like to make sure that when I boot from the USB it won't affect my hard drive's bootloader/partitions at all, and just keep it all on the USB.
Is this correct?
The thing is right that It will not affect your hard drive partitions but you will get option for ubuntu in your Windows Boot loader. you will get entry for ubuntu on windows bootloader. When you will select it you must have attached your ubuntu installled USB drive, Otherwise It will show error.
I would advise you to do a full proper install to your USB and forget Wubi.
Installing Ubuntu to an external hard drive or USB memory stick is a very safe way to install Ubuntu. If you are worried about changes being made to your computer, this is the method for you. Your computer will remain unchanged and without the USB inserted, it will load your operating system as normal. When you connect and boot from the USB drive you will be given the choice to load Ubuntu or your usual operating system.
Have a look at this question for instructions on installing Ubuntu to USB drives, the process is almost identical for Xubuntu.