Yes it does mean something. I don't think all your ports are 6Gb\s, could be only the first 4. So 5-6 are probably 3Gb\s. Most motherboards are like that.
In any case, I think the system gives higher priority to the first ones. Usually on a motherboard they will be labelled from SATA0 to SATA3 (instead of 1-4, because they start to count from 0).
You should always connect your most important device (in this case your SSD containing your OS) on the first one (which should be labelled SATA-0). And then your secondary most important (for example a secondary HDD containing your data) could go on SATA-1. DVD burners require less performance and cannot achieve 6Gb\s anyways, so they should be connected in SATA ports 5 or 6.
Now if you...