Modern systems can accept four EIDE devices on the hard disk controller, so there shouldn't be any problem installing both disks on your system at the same time, even if you also have other EIDE devices. Hard disks and CD-ROM drives are typical EIDE devices. Floppy drives and tape drives are usually connected to the floppy drive controller rather than to the hard disk controller.
SCSI adapters are even more flexible and can accept seven devices. If you're lucky (and rich) enough to have a SCSI adapter, you probably already know this, and you probably know which of your devices are SCSI devices! For more information, see the SCSI How-To.
Even the oldest systems can accept two devices on the hard disk controller, so you can still install both hard disks at the same time. However, if you already have another device installed in addition to your hard disk (for example, if you have both a hard disk and a CD-ROM drive), you'll have to remove the other device to be able to install the old hard disk and the new hard disk at the same time.
You must configure the disks as master or slave by installing the disks' jumpers as appropriate. You'll often find configuration information on the disks themselves; if not, consult the manuals or the disks' manufacturers.
You must also inform the BIOS of the disks' presence and of their geometry. Usually, you enter the BIOS setup program by pressing a key during the system boot-up. Here's what to do for some common BIOSes:
F2 key during Power-On Self-Test (POST)
Del key during Power-On Self-Test
Del, or Ctrl-Alt-Esc
F10 key after the square appears in the top right corner of the screen during boot-up
Esc key during Power-On Self-Test
F1 key during HP blue splash screen
F1 while the square with the wavy lines is displayed in the upper right corner during power-on 
Ctrl-Alt-Del, then Ctrl-Alt-Ins when the cursor is in the top right corner
Ctrl-Alt-S during Power-On Self-Test
For some models, F1 or F2 key during Power-On Self-Test
Ctrl-Alt-Esc, Ctrl-Alt-S, or Ctrl-Alt-Enter
Many older systems require an Installation or Reference Disk.
Reboot the system and login as root. If you use the su command to become the user root, use su -, with the hyphen option.
Does this also apply to other Aptiva models?