They're exactly the same with a different plug. Same interface over a mini pci-e connector. You won't see any difference compared to your S3 ssd.
If you meant you wanted the MSATA ssd to replace the mechanical drive, I'd advise against it. Solely because all your important software (OS, games) will be on the primary ssd, and you can use the mechanical one for storage. (This is assuming the mechanical one has a bigger storage capacity than the MSATA ssd. If they have the same capacity, the MSATA ssd will perform faster.)
They have the same performance given the same specs on the drive itself. But, there's not a lot of choice with mSATA. mSATA doesn't really have any offerings that can compete with high end SATA3 drives like OCZ Vector or Samsung 840 Pro. But, to answer your question, it depends on what S3 drive you ordered. Tho, at that point it would be more beneficial to get a faster S3 ssd.(Purely in terms of performance. If you want to run both that's up to you)