The video card shouldnt matter for when you are installing windows. There isnt a driver being used like that, so it doesnt matter.
As for the drives, put the one you want to be the bootable drive in the master position of the primary IDE channel. Make sure the jumpers for it are set to Master. Plug the other one in on the slave position and set its jumpers to Slave.
One more thing--when installing windows, make sure you have the SATA drivers for your mobo on a disk. When the windows installer is loading and asks you to hit F6 to load any SCSI drivers, do it and load the SATA drivers.
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"Good people do not need laws to tell them to act responsibly, while bad people will find a way around the laws."
--Plato
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