I finally figured out how to make all the drives sing happily, switching back and forther between IDE/AHCI and RAID for my SSD boot volume running Windows 7x64. I though I would take a few moments to share what I learned since it tooks weeks to manage and should have taken no more than an hour.
rather than provide some step by instruction - though I will illustrate a few pivotal step, this is a concept guide, since this is what I was lacking.
Concept 1: It doesn't really matter how you install the OS on the volume, you can make the switch either way later, as long as all the drivers for both interfaces are installed and the registry values for them are loaded to an active state.
Concept 2: Non-RAID volumes can be accessed as AHCI volumes while attached to the RAID interface. These are made available through the ahci64x.sys driver which provides both RAID and AHCI support for non-raided volumes.
This critical concept:
Concept 3: The legacy RAID Option ROM does not require you to make the volume RAID0/5/10/JBOD. You can set the volume to RAID Ready and just inititalize it. This will rewrite the MBR for which you will have to repair on reboot, but does not impact your data. You can remove the inititalization the same way and return the volume to AHCI/IDE, but you MUST inititalize for RAID, or uninitialize (delete the LD volume from the RAID array) if you want to return to AHCI/IDE. ** This does not destroy your data if RAID Ready is the selection. If you move a volume out of a 0/5/10 array you will lose your data. **
Here is what I wanted:
a. An SSD boot drive on sata port 5 that I ccould toggle between RAID Ready and IDE/AHCI
b. A data volume in AHCI on sata port 6
c. 4 X RAID5 backup volumes on sata ports 1-4 (not going to cover this as it is a no brainer)
Steps I took:
1. Make life easy on yourself and enable the RAID (1-4) ports before you install the OS, have the drivers available on a USB volume and insert it when prompted during install. I also enable AS Media in AHCI to support the CD ROM for install.
2. Install OS - I couldn't install as AHCI, it would not format my SSD correcty, so I installed as IDE. SSD on sata port 5.
3. When all installed, verify in device manager that all the drivers are loaded. I plugged in one of the 4 RAID drives I had previously in a striped set so that it would appear to the RAID host controller.. dunno if this is required, I don't think you need a drive attached - but if so, plug one in and initialize it as RAID Ready if you need to.
4. Regedit - msahci=3 pciide=0 (for my install) <- you may reverse these if installing as AHCI instead of IDE - you can always switch. ahci64x=0.
5. backup - acronis partition image to D drive on sata 6
6. Move SSD from port 5 to port 1. The Legacy RAID Option ROM would not create a new LD to sata 5 for some reason - had no problem on port 1. So simply move it, make RAID Ready, Inititalize fast - takes about 20 mins on a 128GB SSD.
7. Move back to port 5. The RAID Option ROM required me to reinitialize the drive on the new port, but at least now it would work with it, now that it was RAID ready. This time, change the inititalization to none and save. You are now RAID Ready on port 5.
8. BIOS - change all channels to RAID - reboot
9. BIOS - Set boot order for RAID_VOL to boot
10 - profit.
11. Want to reverse - make sure the pciide=0 is always set. Uninitialize (delete LD from the array). Set Bios back to IDE and reboot.
Here is what my device manager looked like after fully booted into RAID:

Notice the Storage controllers are RAID only, IDE ATAPI only lists the AS Media Controller and Channels, and that the drives are all suffixed with SCSI. Mind you that these were formatted and defined as IDE/AHCI and only the C Drive is initialized as RAID Ready.
Hope other find this usefull..
Ranger
CPU:AMD FX-8350 BE @ 4800Mhz C5F 1803
Clocks: FSB: 200x24 NB:2400Mhz HT:2400 Mem:2133Mhz
Voltage: CPU:1.50 NB:1.20 HT:1.20 Mem:1.65
Memory: 8GB Gskill DDR3-2133 (F3-17000CL9D-8GBSR)
Storage: sysvol: 2x256GB Transcend SSD RAID0 (amd_sata) Game: 128GB SSD Data: 2TB SATA
GPU: EVGA GTX 680 SC+ SIG 2GB 1254/3105