I'm still having a hard time figuring out what you issue is but I'll give it a go anyway. So with your monitor connected to your dedicated video cards DVI port, you don't see your BIOS menu? The onboard video card is disabled as soon as an add in card is detected, that's why you have to remove it to use the motherboards VGA connector. What other ports are on your add-in card? Also, there may be a BIOS setting to tell the motherboard what card to use first. My BIOS has an option to set the PCIe as first choice for video. My BIOS shows when I have an add-in card connected. It will switch monitors depending on how many I have connected and what port they are on. My BIOS POST screen always shows on "a" monitor though. Is your monitor connected DVI to DVI?
EDIT: I run three monitors on a NVidia GT 640, DVI, DVI, and HDMI to DVI.