Hi SparkyJoe-
I just built a similar system (ASUS P5WD2-E Premium), which also has an on-board RAID controller and the Intel ICH7R chipset.
What we found was- finding RAID compatible drivers for the on-board chip was problematic at best. The mainboard CD is bootable and has a utility for making a driver floppy for Windows XP and Win 2000/2003 installation, but neither would see the RAID group we created. It just treated it as a SATA controller with all RAID drives visible but no RAID volume at all. This was a problem for us as we wanted to put the OS on a RAID device.
As we only wanted RAID 1 (or RAID 0), we just said "the heck with it" and disabled the on-board RAID controller and used the Intel ICH7R- which worked with flying colors. XP, 2000 & 2003 see the RAID volume vs. the individual drives this way, as well as the CTRL-I bios setup-screens built-in to the Intel Raid Utility are very nice and full featured. This also allowed us to remove to other raid controller/hardware entirely and save some address/rom space as well.
The main advantage to struggling with the Asus 3rd party RAID controllers is mainly if you want beyond RAID 0 or 1. The on-boards will support additional RAID forms, but at the cost of additional/non-standard drivers and processes. If you're not choosing to install the core OS to a RAID partition, you can pick & choose however you want as once the OS is installed, you can add RAID drivers for Windows that will allow maintaining raid groups. But if you're planning on installing the OS on RAID or don't need anything aside from RAID 0 or 1, I'd say just use the tried-and-true, Intel ICHxR chipset as it's solid, has great support and performs fantastic.