One thing... don't panic TOO much...
When using Prime, the ammonia will still show up on the typical drop test kit. It has been bound up, but is still available for plants or your tank's biological filter to use. (Is your tank planted?)
Sometimes, if you do TOO many water changes, you do mess with the tank's cycle.
Did you change the filter cartridge? If so, you've sent it into a mini-cycle.
Prime also helps bind up the nitrites and nitrates.. but I'm not sure how much you need to use...
Most people on here do not change their filter.... the brownish gunk you see is the bacteria you need. If it is restricting water flow, rinse the filter in a bucket of tank water.. never chlorinated water, as that will kill off the bacteria you need.
http://www.seachem.com/support/FAQs/Prime.htmlThis link has some information on Prime... but as you see, they don't really understand it either.