I would start with them unplugged, this gives a 24db/octave rolloff. Plugging them changes it to 12 db/oct. Although it never hurts to try it both ways with your system, in your room, etc. Have you listened with them plugged vs unplugged? Set them they that sounds best to you. I've never tried the plugs on mine, I like them ported!
The crossover controls on the sub work together for whatever slope you need.
Optimizing subs takes a little trial and error, but well worth it once they're dialed in!
The subs will make the Sapphires a killer- full range system. Not that they're far from it though.
JK