I would use the Intel sata3 for a raid connection and the Marvell for just a single SSD connection. When using a single SSD there is not that much difference between the Intel and the marvell. The thing is that the Marvell chip is just there to run the sata3 ports and the Intel is running from the south bridge which does have other things it is running.
Since you do have both Intel and Marvell you could do a benchmark on each one and see if by some chance one is better than the other. It won't mess anything up by unpluging from one and pluging into the other , that way you could see for yourself if there is any difference. Just because you were to plug it into the marvell port doesn't mean it's perminent.