When you couldn't get it to work properly at first, which part didn't work? Did the drive not get seen in the BIOS or would Windows not load or what?
From a BIOS perspective, you can usually get access or at least "see" a hard drive connected to an expansion card. This depends on whether or not the chipset (in this case the Silicon RAID chip) has low-level support and/or bootable BIOS support.
From a Windows perspective, it's always a good idea to install an expansion card before you start connecting things to it. This is no different from trying to install a USB 2.0 PCI card while having a printer attached to it. Install the card first, using the IDE driver, and then you can attach drives to it.
As for removing the DDO... well, I guess I would keep trying until something works! But an IDE card with RAID support usually has a bootable BIOS of its own, so I would think you could do that at any time, as long as you don't get Windows involved.