I haven't done exactly what you are proposing, so hopefully I won't miss anything. And it'd be best to give details on what each disk does and the exact disk controller chips involved for the reasons that I'll detail below.
Remember that XP/2003 (the basis of WHS) can't adapt well to a new disk controller connecting the boot disk. If neither of the disks you mentioned is the System disk, then there shouldn't be a boot problem. But if one is a System disk, and if the old disk controller drivers won't work with the onboard disk controller, you may have a boot problem. This can likely be fixed by performing a reinstallation of WHS (NOT a new installation, which will cause the loss of all indexed data from the new WHS system).
No matter what, make sure that the WHS System disk is at the top of the BIOS boot list after you've moved around the SATA ports. It's not really necessary right now, but if you ever have to do a Reinstallation of WHS, you'll need the old System disk at the top of the boot order or the WHS recovery routine won't detect a previously-installed WHS system and will only allow a new installation of WHS.
Depending on the disks and the controllers, it might be best to consider a Reinstallation of WHS. This would give you the chance to introduce the drivers for the disk controllers as you do the reinstallation, so you can be sure that the System disk and the data disks will be readable by Windows as WHS attempts to recover the system and the data.
Note, though, that WHS will lose any client PC backups if you do a Reinstallation. If this is important to you, you'll need to "back up the backups" and move the backup folder to the "new" system after reinstallation of WHS. This procedure is covered in Mcirosoft's white paper on how WHS backups are managed.