What version of windows server are you trying to install?
I know they do not have any onboard SATA and rely on the SCSI RAID and onboard IDE for drives.
if you are booting anything Server 2008 and up it will be easy.
How exactly is your setup? The times I have installed server 2008+ this is what I do.
Install SATA card, install SATA dvd drive, boot off DVD. When it is asking for a driver put the correct drivers on a USB drive from another PC and then plug it in to the PE and then browse to that folder for the drivers. It should detect them and then continue the install. Once the install has gone though they drivers will now be in the Server 2008.