2nd SSD as main boot disk, what do I do with old filesystem?
If you want to put your most-used files on the SSD and the less-frequently-used files on the HDD, you could make your own Fusion Drive. I'm paraphrasing the instructions here:


Take a Time Machine backup of everything. THE FUSION DRIVE-MAKING PROCESS WILL WIPE BOTH DRIVES!
Make a bootable OS X USB drive. If you can't, that's fine, but doing so will let Recovery HD live on the SSD. If you don't care about that, you can skip this step.
Boot into your brand-new bootable drive (or Recovery HD, if you don't care if Recovery HD lives on the SSD or the HDD).
Open Terminal and run diskutil list
Take note of the identifiers (the "disk#s#" designations) of the drives you want to use as part of the Fusion Drive. If you're in a bootable drive, you can use the entire HHD, but if you're in Recovery HD, you'll have to only use the partition that is neither EFI nor Recovery HD.
Enter the command diskutil coreStorage create [arbitrary name that you won't have to look at anywhere but in Terminal] [the disk identifiers, separated by a space]
When that process is done, one of the last lines of the output should be Core Storage LVG UUID: [long string of letters and numbers]. That long string is your Logical Volume Group's UUID, and you'll need it for the next step.
Now run the command diskutil coreStorage createVolume [the UUID from the last step] jhfs+ "Macintosh HD" 100%
Once that's done, your computer will officially have a single "volume" named Macintosh HD! Now you can reinstall OS X on it and restore it from your Time Machine backup, and it'll automatically migrate files between the SSD and the HDD based on the frequency of their use.


Good luck!