If you are upgrading your controller card, look and see if your floppy drives are connected to your old controller. If so, you will need to buy a new controller that lets you connect your floppy drives.
If you are upgrading to a SCSI controller card, make sure your CD-ROM is not running from your sound card's controller. You can only have one SCSI controller in your PC. Most likey, disable the SCSI controller on your sound card, and connect your CD-ROM to your new SCSI hard drive controller.