I am just not able to install Libranet on my hdd.

Here is the config....
20gb hd, main hdd.
IDE PCI card.
|_____ 1 - 110 GB HDD
|_____ 1 - 114 GB HDD (backup of first)

When installing with everything installed, Libranet is not able to find hde1 (20GB), it sees it as a third hard drive. It wants to install on the 110Gb drive.

I can pull the IDE card and install Libranet on the 20GB which is now identified as hda1. However when I install the IDE card back, it is not able to find the boot files.

Ubuntu did not have a problem with this... it identified the 20Gb as hde1.... so when installing the IDE controller back, it still is using the hde1 as the boot hdd.
Using Libranet 3.0
Any suggestions?

Sounds like the controller is getting first IRQ over the the motherboard IDE. I assume we are talking about the 20gig connected to the motherboards IDE connector. Some things to try:
Put the IDE card in other slots. It may use a different IRQ that causes the motherboard to tbe first.
Does the controller have any jumpers or software bois controls at boot up?

It does have jumpers... don't know what they do. No directions when I go the card. A nice cheap card.

It does have it's own bios.
I will try switching the card to another slot.

If not sure of the make and model then using a Live CD like knoppix you can use the command ' lspci 'to get info on the hardware.

Look in the BIOS setup for the computer. First notice how the computer itself views your ide drives. Second, you may be able to alter the boot order of these drives, in the case the two drives have MBR bootstrap loaders installed.
After you reinstalled the other harddrives, the drive references may be different, so /etc/fstab for one example needs fixing up. You may need to change both the /etc/fstab entries and either the /etc/lilo.conf or /boot/grub/menu.lst file. In the lilo case, re-running lilo as root is a must. This could entail booting up with either a rescue disk, or a live distro; then chroot'ing to your systems root parition; editing the files that need changing.
And for lilo, you may need to mount any partitions that are referenced in the /etc/lilo.conf file. ( Sorry, I don't know which boot loader that Libranet uses by default ) If an error occurs when running the /sbin/lilo program, the mbr won't be updated with the new drive information that you need to boot. So it is important to get it right before rebooting.

Another option, if using grub is to use the grub shell to boot up. If the drive references in /etc/fstab are off, you might be dumped into a root maintainance shell, where you could perform your fixes.

If you decide to re-install instead of fixing what you have installed; does the installer program have an "advanced partitioning" option, so that you can partition your drives yourself rather that using the installers defaults?

P.S.
I wasn't clear with this sentence:
"When installing with everything installed, Libranet is not able to find hde1 (20GB), it sees it as a third hard drive"

The "not able to find" part contradicts the "it sees it" part. I hope that didn't lead my answer in the wrong direction.

Ok, I have completed the install of Libranet on the 20gb hdd with the IDE card installed and have tried it without the card installed. Libranet, when I reboot the machine after a complete and new install, is now "seeing" the hdd as hde1 instead of hda1. During the install without the IDE card, Libranet saw the 20gb as hda1. Poweroff, install the IDE card, no boot files. Try to install with the IDE card and drives attached and Libranet sees the 20gb as hde1. I installed everything to hde1 and guess what... on the reboot, does not find the boot find and has a kernel panic.

Libranet uses Grub. And of course I am not able to edit the fstab file until I boot the OS.
I could use a live CD, but how will that help on the initial boot?

Ok, I have the model information by using Knoppix cd.

RAID bus controller: Silicon Image, Inc... blah blah...

What now?

I got it working... here is what I did. I did it a bit different than before..

1. Unplugged the two HDDs that are connected to the IDE card.
2. Booted and installed Libranet... everything looks good.
3. Rebooted and checked fstab and menu.list... still good.
4. Poweroff, plug in two HDDs that care connected to IDE card.
5. Boot up... is working.. finding everything.
6. On desktop - updated fstab for both hdds and mounted both HDDs.
7. Now doing a Libranet upgrade...

I am glad Libranet is working... I hate Ubuntu as a server.

Your BIOS may not be able to boot to a drive if it isn't one of the first 4 drives.

The grub shell has auto-completion, so you can actually search for the kernel and initrd file and boot that way.

Here is a good manual for grub which might help.
http://www.gnu.org/software/grub/manual/grub.pdf