OK, I think I see your problem here. You imply you are setting up two SSD's within the system. Is that correct? If so I have some bad news for you, the EFI and OS-X currently doesn't support dual SSD's.
As to your config I would recommend setup up a Fusion drive with the HD & SSD and give that a try. That way you'll gain the best performance for both booting and small length recording.
As for long recording at full depth (over sampling) then you'll need an external 4 disk RAID array using the fastest I/O the system offers. In this case you have a ThunderBolt port on your mini which should do here. I would setup two partitions on the raid set, the first a scratch space to record and the second the location to store recordings for edit. Keep the scratch as empty as possible so it stays contiguous.
As to SSD's sorry to say the current SSD's are not the ideal storage for video or sound recording. While they are fast in retrieval they are not as fast as disk drives (RAIDED) in recording. Besides, the constant churning of data will wear them unlike a disk solution. You will still need to manage your disks making sure to wipe them down (unlike defragmentation of a single disk which you can use a application to clean up, you need to delete all the files fully on the RAIDED disks).
The new Mac Pro coming out sometime next month maybe a better solution if you want a SSD solution. But even with it I would use RAIDED disks to hold the recordings.
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