Yeah, you will need to reconfigure the Grub setup after you move the drive to a controller card. You can otherwise move the drive around without any problems (see below).
While you have FC3 running, make a Grub boot floppy as is described in the Grub manual (http://www.gnu.org/software/grub/manual/grub.html
) in the “Creating a GRUB boot floppy” section. Then, after you put in the controller card and swap the drive to it, follow the section “Installing GRUB natively” by booting from the Grub boot floppy and then using the commands “find ...”, “root ...” and “setup ...” as are described in the manual.
Regarding swapping the FC3 drive around later, the way FC3 will set up the drives in /etc/fstab and in /boot/grub/grub.conf will use the “LABEL=” format to identify the partition(s) by name, as opposed to the “/dev/hdxy” format which points to specific devices. As long as the FC3 partition labels are not used by any other partitions in the system, you can put the FC3 drive anywhere that Grub can find it and FC3 will boot/run fine. Of course, the MBR Grub Stage1 loader does need to point to the correct boot partition, hence the reason for making the Grub boot floppy.