I have 250G drive hooked up to my Time Capsule with some Flip Videos on it that I have offloaded from my MB. I want to have these backed up to the TC. Is there a way to do this using time machine. Right now I just copy over the files.
No, Time Machine cannot back up from a network location.
CarbonCopyCloner (donationware) can, and the ChronoSync app (about $40, I think) can.
However, putting other things besides Time Machine backups on the TC's internal HD presents some conflicts. See #Q3 in Using Time Machine with a Time Capsule for details and some workarounds.