There is one very important thing to do and that is to enable TRIM support
sudo trimforce enable
In OS X prior to Yosemite, you had no way to enable TRIM on 3rd party drives. But in Yosemite and later (10.10 and on) Apple included the ability to enable TRIM on non 1st Party (OEM) drives.
From Apple Insider:
Part of the ATA standard, TRIM helps optimize garbage data handling in SSDs by earmarking files no longer in use for permanent deletion. Unlike conventional spinning hard drives, SSDs perform erase operations before writing new files, meaning multiple erase/write operations could create a backlog of garbage bits that gradually slow the system down.
As for cloning my drive, I am not a fan of simply copying the image of a drive from one to the next unless I am doing disaster recovery. What I would do is a Time Machine back up, do a fresh install of the OS of my choice, then migrate the data from Time Machine.
Is this more time consuming? Yes. But I have found it much more reliable.
As for your setup, I would probably create my own Fusion Drive. Instead of buying a single HDD, there are 2nd hard drive kits you can get that allow you to install two drives in the Mac mini. The instructions on how to install are on iFixit.com
This (IMO) gives you more flexibility. You can use them as two separate drives or create your own hybrid/fusion drive using CoreStorage
As for your drive choice, (also IMO) I would say away from anything Seagate. I prefer Western Digital just based on the number of failures I have with Seagate drives. I have found WD to be much more reliable. It also seems I am not the only one according to USA Today