It will boot with AGP or PCI,
The BIOS detects whichever..
However..if you goto use 2 cards PCi and AGP for dual monitor, you will have to set "Vid Intle" or whatever it is to AGP before you insert the PCi vid card, other wise it will boot off the PCI card as teh default card.
I have the same board for my MP3 machine, I have used a V3 and Nvidia Rivia TNT in it at the same time, But the V3 died on me...
So yes, it will boot err post with a PCI or AGP vid card.