First you may want to read up a bit on Apple recovery services, Apple TN: OS X: About OS X Recovery
From the sounds of it you reformatted your HD after it appeared to die from the recovery partition. If that is the case unless you have backed up all of your stuff you may have lost access to the files. If you still need to get to something you still have a small window here to salvage the files. What's most important right now is not to alter the HD as any new file could overwrite what are now hidden files. A good disk utility like Drive Genius can recover the files still, but the more you alter the disk the less you will be able to recover.
OK, lets say you are beyond that issue and just want to move on replacing your HD.
We have a very large pool of Mac systems desktops & laptops. At one point we did the dual drive setup on the laptops to give them some zing and make managing apps easier.
For a while it worked, but Apple changed things enough with the intro of the Unibody design'ed MacBook & MacBook Pro systems the dual drive setup was not going as smoothly as it once was.
Also, at the time hybrid drives (SSHD) started to show up. Yes, the first generation had some issues (which I think is what you are thinking about), but the 2nd & 3rd generation drives are much better!
With a better SSHD's we have moved onwards dropping the dual drive setups and going only with SSHD drives with all of our HD based laptops (like yours).
We have now well over 200 systems with SSHD's in them and any dual drive systems that come in for service gets converted to a SSHD as well. They are holding up quite well and while the performance is not quite as good as a straight SSD its dam close.
While it may appear nice to do away with the optical drive the drives I/O has issues running a HD or SSD in many of the unibody HD models. Here's a reference on the issue from OWC but it makes no difference who's carrier you use the issue is the same. Go to the bottom notes area and review the section in Red OWC Data Doubler.
In addition to the SATA compatibility issue most of the Apple HD's don't have crash protection so moving them over to the optical bay puts the drive at risk of crashing as there is no crash protection services off of the optical drives SATA port.
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