I've removed the 6 GB/s SATA3 cable and reconnected the internal drive with a 3 GB/s cable into the first SATA2 slot (Port 0). The DVD in now plugged into the last SATA2 slot (Port 5) with the 3 GB/s cable that it was already using. I then set Configure SATA as...RAID & disabled the Marvell SATA Controller via BIOS. Booted right into Windows and Intel Rapid Storage now recognizes the drives properly with the HDD in Port 0, the DVD in Port 5, and Port 1-4 open.
So far so good.
Just finished backing up the drivers and applications that I've downloaded over the past couple of days (not forgetting about Favorites that I've bookmarked as well). So I'm good to go this morning and I'm hoping for the best. I've come up with the following drive structure and I'm felling like it should meet my needs rather nicely:
C:\System (100 GB)
D:\Games (400 GB)
E:\Data (500 GB)
F:\Backup (500 GB Internal USB) <-- I ended putting this inside the case and running the cord out an extremly small, already exiting hole in the back. So I'm calling it an Internal drive

G:\Vault (250 GB External USB) <-- This one only comes out of the desk drawer when needed.
I'll pay more attention to space usage over the next couple of weeks and possible adjust accordingly (like maybe bringing the C drive down to 50 GB). Otherwise, I feel good rather positive about this and I think that it's time to commit.
On a sadder note...after much research I have discovered that I had the wrong data sheet for the 500 GB USB driver. Turns out that it's not 3.0 compatible so the 34 MB/s is actually considered above average for that drive. O'well, I've never complained about its overall performance, reliablitiy, and usefulness so I'm not going to start now.
I'm off to start the process. Again. Finally.