I have a marty sub with an inuke 3000dsp in bridged, I also have 2 PA-120 powered subs. Can I run the 2 PA-120s off of the iNuke 3000 also. I want to be able EQ the PAs with iNuke software.
No, you cannot run the PAs off of the inuke. I have a very similar set up. I built two large ported subs, very similar to the marty. I am also running an eD a5-350 and a pa-120 in that room. My inuke runs my DIY subs and I use a behringer feedback destroyer 1124 to EQ the two other powered subs. I EQ the group as a whole, which means I run the same filters on the inuke and the bfd.
My suggestion would be pick up a behringer 1124 and use that to EQ the PA subs and leave your marty on the inuke.
It'll take some time and messing with sub locations, but in the end it can work out with some diligence. I arranged mine following the geddes method.