From my rather limited understanding, when you place an agp card into the slot it will automatically turn off the on-board graphics and then start communicating with newly installed agp card. I did a google search and didn't find anything about conflicts between the nforce2 and radeon chips. I didn't look past the second page, so there might be something somewhere. If so, it must not be a major problem.
Update: is your mobo an Epox board? There seems to be some kind of bios related problem between radeons and the mobo. See this website for more details and some useful links.