First off...
Don't use the marvell SATA controller.. it's a poorer performer than the intel sata controller... i'd recommend getting off that marvell controller ASAP as that controller only runs on a single 1x PCI-ex lane which is terrible even for a single Standard Hardrive... obviously running in IDE mode isn't bad.. but they are mostly there for hot swap external hardrive solutions or just stop gaps. Actually in the case of filling all the ports on the main intel sata controller with hardrives.. it's specifically handy for plugging in a dvd/cd rom drive when you've ran out.
Otherwise disable it...
Move the Hardrive onto the primary port of the intel controller and disable the marvell..... and then try and get everything situated to either ahci or raid.
you'll have the best performance and capability that way.
As for installing games outside of the C Drive.. this hasn't been a problem for nearly 15 years... For example when you first install steam..... go through the custom setup options and direct the installation to D:\Steam and it'll install steam to that folder and all the games that are part of steam will be installed where they should be inside the steam folders as usual.
Other games just select custom install and direct it to it's own folder on the other partition to.
Even REALLY really cheap terrible games that people tend to pull out of the bargain bin or cereal boxes don't have problems with this. I know SOME very very old dos games occasionally had stupid directory structure issues.. but otherwise.... works just fine. Patches install just fine... etc.. and so forth... like i said.. i haven't heard or seen a game having issues due to where it was installed to... the parts that need to be placed on the C drive will still be placed there... for example skyrim will still place the configuration and save files in the documents folder.... even if you move the documents folder around to different locations or different drives/partitions... it'll still know where to fetch it.
Back to the whole raid thing...
As i suggested.. the IDE/AHCI/RAID fuctionality is simply a settings.... i suggested raid as it ensures everything is running at it's peak capabilities.
I didn't suggest that you technically setup a raid array with it, you don't need to, although if you wanted to.. having it setup already would save you a little grief in the long run.
ignore the following aside from just giving you a little crash course as was previously somewhat stated in this thread regarding the raid array system itself IF you decide to raid drives together Spoiler
Raid 0 array is the fastest, but doubles your chances of losing all your data.. because if one drive fails.... game over... It combines the performance/speed/capacity of all drives. (2x1tb = 2tb seen as a single drive...)
raid 1 is mirroring, great for on the fly backups without really any performance impact to speak of. 2x1tb drives will be seen as a single 1tb drive (the other will be hidden)
Raid 5 is combination of both raid 0 and raid 1 but requires a minimum of 3 or more drives to work, the more drives you have the better the raid "1" part of it works, ensureing that your not going lose stuff if a single drive fails.
Regarding your performance loss.... I'm betting that's likely due to using the Intel Matrix Storage software rather than the software i posted a link to which is the newest Rapid Storage Controller Software.
You did install the inf update prior to that as well right?
Using synthetic benchmarks isn't my idea of a great way to really benchmark.. and i know there really much beyond that to really know for certain.. but i do know for a fact that with intels controller being used, IDE is significantly slower than ahci and raid....
also don't forget that with NCQ being enabled and working, that random multiple accesses will be significantly reduced in time.
and your right, you shouldn't be able to access the CTRL+I menu of the intel raid system if you only have 1 hardrive installed.
However intels support for RAID mode with a single drive or multiple hardrives and SATA CD/DVD/BR-rom/rw drives has been supported for several years with full performance and no issues. If there is a problem, it's likely due to the optical drive..... not the controllers fault.
I give a short run down again just to clarify how i would setup:
Ensure the latest bios has been updated
Set optimal settings
Disable all sata controller excluding the intel one
Set intel sata to RAID
Ensure that the Hardrive is in sata port 0 (the first port should be SATA II 3gbps using a SATA II 3gbps cable) and that the optical drive is sata port 5 (the last one using sata II with a SATA II cable)
Boot from windows disk to install windows OR boot into existing windows IF you've already prepared it for being able to boot from the changed setting.
Emediately install the Intel INF Update utility from intels website for best results
Reboot
Install the latest Rapid Storage Controller Software/driver from intels website for best results
reboot (may require 2x reboots)
Install the other device drivers respectifully and proceed with latest updates.
And don't disable the intel rapid storage startup service or startup process... they have other benefits including reporting smart issues directly to windows which can inform you of an impending issue with the drive.. or other drives. (it uses absalutely nothing for startup time or resources... it's got a delayed start of about 1-5 minutes to ensure it's not slowing you down which is also nice)