Barring individual performance differences between the two drives in question, there are no differences between an MSATA SSD installed in the mPCIe slot and a 2.5" SSD installed in the drive bay; they both consume the SATA III lane that was dedicated to their location.
My personal preference would be to use the mPCIe slot for a MSATA SSD to use as boot/system device so that I have the 2.5" bay for a large (typically non-SSD but perhaps bybrid) data drive...
As I am going to use the mSATA for a HTPC, it would seem that it would not require much storage space - a few programs and files. Would there be any problem with partitioning the drive as a boot drive and a home storage drive? Or, would you recommend using a smaller mSATA only for booting and use a 2.5 drive for storage? Thanks!
It's really a matter of personal preference and the way you plan to use it. You have to weigh the performance vs. cost question. I have more than one NUC and the usage for it largely determines the drive configuration. For example one is used for a Windows workstation. I have a 180GB mSATA in it with Windows installed. It works perfectly.
I also have a taller unit (supports both SATA and mSATA) that I use for an HTPC. That one has a small (60GB) mSATA drive with Windows installed, and a larger (320GB) SATA drive for data. I use the SATA drive to store movies, music, pictures, and recorded tv. It's just a cleaner way to set it up. Also, if the need ever arises I can just pull the SATA drive and attach it to another system.
There was a big cost benefit for me using the dual drive configuration. I was able to get a super-high-speed mSATA for relatively cheap because of it's small capacity, and a higher capacity "platter" SATA drive for storage for a good price as well. The storage drive doesn't need to be as fast because I'm not running my applications or OS from it. Combined I have 380GB of space with a total cost of less than $100 for the drives. I wouldn't be able to get under $100 for an mSATA that large.
Sorry for rambling on, but I hope this helps.