The 2 flexports are for multi dish setups, in your case you have one dish, so these will go unused for you.
The markings you speak of on the other four remaining ports, are for when the LNBs are directly connected to this 6x8 multiswitch, BUT, with a AT9 or PhaseIII dish, there is already a multiswitch inside the dish itself (i.e. your new 6x8 is _actually_ connected to the dishes built-in multiswitch, not the LNBs), so the markings do not apply, so it won't matter, the built-in multiswitch will negotiate which LNB is which, all four coax coming from the dish have already been multiplexed (via the built-in switch), thus, the 4 coax from the dish are identical in that all have the ability to control all the LNBs (which is why they can go directly to a receiver). If you were connecting the LNBs directly to the 6x8 (which btw is NOT what you are doing), THEN it matters.
A good (if not simplistic) way to think of it is, that the built-in switch is the 'smart' switch, and the new external 6x8 is relegated to being a little more than a dumb 'port extender' of sorts.
If it makes you feel better, and perhaps might still be a good thing (maybe you'll use them for other things later), or for ease of replacement if one gets damaged, go ahead and mark the coax ends with a color code, but there is no need to mark them 18v/13v or 110/101/119, etc..