First thing to try will be a look in the BIOS to tell it to use the AGP card first instead of the PCI card. ( if it's the same as the board I have here.) It should be in the integrated peripherals section.
There may also be an option to disable the on board chip in the peripheral section.
Another thing to watch is that you may need to tell it to update it's settings in the Plug & Play section, so that the motherboard tells Windows about the new configuration.
Not sure on that mobo, you might have to do some changing of the memory size allocated to the on board chip, in some cases, it conflicts with the AGP graphics card, which can lead to the beep issue.
A long time ago, ATI cards and a sound card used to conflict for an IRQ, but I think that one has now been sorted out and is no longer an issue.
another possibility will be to power down, remove the ATI, reboot but get into the machine in safe mode, delete all the graphics adaptors and monitors before power down. Put the ATI back in, power up and let Windows sort itself out from there.