Will any software allow me to write to media after making it bootable?

I have a flash drive that I made bootable using the ubcd2usb tool on the latest UBCD release. Problem is, when I try to add files to the drive through Explorer (Vista), it seems to corrupt the drive’s ability to boot anymore. What I’m wondering is if there is software out there that will allow me to write to the flash drive in a certain way or to a certain location to allow me to write new files to it while still keeping the files necessary for booting off of it and running UBCD intact. I’d hate to not be able to do this as UBCD only takes up 115 MB on the flash drive.

Thanks.

I never used that software but is there a way to make partitions when you make it so you can have a place to put your files so you have one partition with the boot files and one to add your own files to?