Upgrade HDD to SSD and use PCIe as second hard drive?

If you currently have a Fusion Drive setup (have the PCIe SSD installed as well) you'll first need to break it to switch out the HD for the SSD. You won't be able to re-create the Fusion Drive setup with two SSD's in the system. Here's how thats done: How to split up a Fusion Drive

Here's the IFIXIT guide you'll want to follow to swap out your HD for a SSD: Mac Mini Late 2014 Hard Drive Replacement.

While you don't need to setup a bootable OS installer to install the OS as this system supports Internet Recovery it will be faster setting up a bootable USB thumb drive as an OS installer. Or get this: Startech 2.5" SATA to USB adapter which will allow you to prep the SSD using your current HD. Here is a good reference on the startup commands: Startup key combinations for Mac.

Just take your time and don't force things! Be careful in disconnecting the cables as some of the small SMT components can be damaged or pulled off if you don't use care.

Many people get confused on what they are buying. So I just wanted to cover that issue in case you had that model. When you open the system if you see this then you have a PCIe SSD in your system. If you don't you're good!

As to using a SATA SSD in this system we have upgraded quite a few with no issues! Its just a plug & play situation. No other hardware alterations are needed.

The only rub is setting up the OS after installing. That was the major point in what I spoke about here. You have a few different ways to do it and you might need to consider which way you go.

Update (01/16/2017)

OK, then you do have a Fusion Drive!

So follow My first point as you'll need to break the fusion set before you alter the drives. Once thats done you'll see two discreet drives the (HD & SSD that make up the fusion set). Then you can replace your HD for a second SSD.

If you where thinking of re-joining the two drives (SSD & SSD) into a Fusion Drive you just won't gain any benefit and just confuse the poor system on which is the SSD as both are!

You also seem to be confused on what your storage will be (size wise). As you are taking the HD out you will only have the custom blade SSD left in the system which is only 256 GB in size (the HD is 750 GB on the 1 TB Fusion Drive).

So your re-configured system will be 256 GB + 512 GB for a total of 768 GB so your total storage will be less!

If you where thinking of swapping out the custom blade SSD then the Samsung EVO SSD is not the correct drive! Sadly, there is no 3rd party offering you will need to locate an Apple spare (very expensive) or a used unit off of eBay.

So in a nutshell I don't think this is a wise direction for you. I think an external Thunderbolt RAID'ed SSD set would give you the speed I think you are looking for and is a lot easier to deal with.