what are you using to test the throughput of your server? i recommend Diskwriggler:
http://www.xdt.com.au/Resources/Downloads/and use something like this:
diskwriggler -NTSC -C -t -n 4000 -o \\192.168.0.11\disk-0 (input your location of diskwriggler and your server address and name)
unless you have a 33 bit/33 mhz pci bus, you should be fine with the IDE card and 1000bT card on the same bus (alternatively, most PCI setups have at least on slot separate from the others, so if you make sure the NIC and the IDE card are on separate buses, there will be no bandwidth sharing.
on my setup, i can saturate the built in gigabit NIC or my PCI gigabit NIC - i have 33 bit/ 66 mhz PCI (max throughput of 266 MB/s)