Ive got 3 optical drives and 2 hard drives. I want the optical drives connected to the motherboard and the hard drives running off the controller card. When set up like this the computer wont boot. I want it like this because EZCD 6 wont work if any optical drives are connected to the controller(known bug). Do I have to do something in the BIOS? This is a Promise card and the documentation is horrible,

A solution might be to have the HD with Windoze on it as Master on mobo-IDE1. Attach the least-used optical disk as slave to mobo-IDE1. The other 2 optical disks to mobo-IDE2.
The second HD could then be attached to the Promise card.
If that card has its own BIOS, it may have a setting to override the mobo-BIOS, so that you can start from the Promise-controller.
Probably your best solution would be, to ditch EZCD6 and use Nero instead.

There is probably a setting in the Promise Card's BIOS to make your machine boot from it. Also, you will probably have to reinstall your operating system, telling it about the controller card when you enter the blue text based stage. You may be able to rescue your current installation using rescue mode and the drivers disk, but I doubt it.

You would certainly be going into your motherboard's BIOS as well, I guess, and disabling anything that tries to boot from the onboard controllers, since you now only have optical devices connected to those.

So, really I think there are changes in the machine's BIOS and in the card's BIOS as well. If the card is so cheap that it does not have one, then basically it does not have a boot rom, and you can't boot from it, only attach drives to it.

One solution in this case would be to keep your OS drive on the motherboard and only attach your second drive to it, since its not likely you will be booting from this other drive ever. You'd be able to keep your 3 optical drives because there would still be primary slave, secondary master and secondary slave available for those on the on-board controllers. You would then attach any additional hard drives to the card.

Onboard IDE
P/M - Operating system HDD
P/S - Optical Drive
S/M - Optical Drive
S/S - Optical Drive

Controller Card IDE
-2nd HDD
-Any additional HDDs.

I assume you would not want more than 3 optical drives (I never managed to keep more than 3 then I was in the period of wanting multiple optical drives in my machine) and you leave the possibility of adding 3 other HDDs in the future for additional storage. (I am assuming a 4 HDD capable card here, yours maybe only supports 2 drive.)

When you start to create bigger and more powerful machines that have multiple optical drives and multiple hard drives and / or RAID arrays, these are the very sorts of issues you will run into often, and you just have to try to think of ways to accomodate them.

The card does have its own BIOS. I set the card in the mobo BIOS as the first boot devise. Foregot to mention that when its set up with opticals on mobo and HDD on card the computer gets past the POST screen and then I get NTLDR missing and no boot. I may just ditch one of the opticals and the card. Its not worth the trouble and Microsoft is hassling me about the number of times Ive activated my XP Pro.

was that HD on the Promise the original bootdisk with Windows in the first partition?
You need ntldr, ntdetect.com and boot.ini in the root of the first-booting HD and boot.ini should point to the booting HD

HDD 0(boot drive) and DVD drive on channel 1 of the controller and HDD 1 on channel 2, CDRW and DVDRW on IDE 2 of mobo. Then formatted both hard drives and did clean install of windows on each HDD for a dual boot.

Maybe do as I suggested first, or hope for someone with a similar setup, that he/she got working. I'm afraid I don't know any further.

I put it back the old way with the boot drive on IDE 1 and secone HDD on the controller. Everything is fine now. I read The drives would perform better if they were on the controller card.

That would be true only if the ATA-speed of the Promise Card is faster than the ATA-speed of the mobo. When 2 drives (regardless of wether HD or CD) are on the same channel, they will both revert to the speed of the slowest drive of that pair.
E.g. if you have an ATA100 and an ATA66 drive pair, they both run at ATA66.
That's why CD/DVD should preferably be on their own channel, not mixed with a HD.