I use APCI and you have to if you want to take advantage of the hyperthreading capablity. I use the 2.6 kernel currently. I would get the latest kernel from kernel.org and compile *without* the debian patches, and then after you get it to work, back it up, and try appling the patches.
Also, when you make your config, make sure you get everything you have including the scsi control that is embedded (?adaptec 9700? if memory serves me) on your board even if you don't use it (you need it for SATA since they run both SCSI and SATA on the same chip) and don't forget to select the exact processor type you have (Intel Xeon/Pentium 4) and if you have dual processors that you enable SMP. Don't forget to add support for e1000 (your intel gigE nic) and you add make sure you enable SATA support.
I love Debian and I'm an active member of the Debian community, but I don't trust the binary kernels. ;-). Most things that important seem still to critcal to let someone decided what I get and don't get in a binary kernel.
Follow the steps on my site if you need any extra help. You can skip the part about knoppix and chrooting the drive.
Also, prepare for disapointment. It make take a while until you get a good build. If you get stuck, then copy your ".config" file you are using to etheir here or to my site under the comments or email it to me at zac-(at)-zacbowling-(dot)-com. I check my email and my site more often but my RSS tool will warn me every 6 hours if you post here.
Hope that helps.
zac *dot* zacbowling *at* com