Okay... so I have an Aspire 5560-Sb653, with a dumb problem... that likely has not been solved.
ATAPI is a tunneling protocol for Windows that allows access to the optical drive; however, before realizing the optical drive was running strictly on this I had made a buy of a 250GB Solid State Drive. Clonezilla copied the partition table and the first two recovery/boot partitions with no issues, then hung up. So, GParted confirmed that the tables were as they should be after the resizing of the 500GB down to a size that could fit, ran Clonezilla with partition to partition clone, everything is working fine! 
Now, the catcher that I found was that the system does not like to POST or boot at all with a second hard drive connected to it; however, I do have a SATA to USB connection, only having 3 USBs means that taking one is a big a hit to connecting anything anything else.
So, I was wondering, will switching the mode to IDE instead of AHCI allow the optical drive to be something other than ATAPI, so I can use the caddy... or... here comes the dumb part that an Acer official site is going to hault me and go crazy with risk factors, is there a BIOS version that is compatible with Acer 5560 that will run the ATAPI device as something other than ATAPI? Which, I feel is the only reason that the system refuses to boot with the HD caddy..
Also, will the newest BIOS 1.15 that states compatibility for the Radeon 7xxx cause any issues with my laptop as it is not running the 7 series Radeon?
EDIT: I have found sites pointing to Phoenix 1.28; however, they show the chipset as Intel where as I am on the AMD A6, so reluctant to try it until I find some kind of confirmed information as to AMD/Intel compatibility for the BIOS.
Also, when I go to Phoenix's site BiosAgentPlus shows a chipset of 1705 which there is another machine on here matching that description, but it's a desktop. I really don't feel like paying $30 for this site's alleged updates despite that Phoenix reccomends but does not affiliate otherwise with them.