Ok. The 390ho in a 3cu.ft. enclosure using the inuke1000dsp. I modeled this in some simulation software (WinISD) and you should net around 95db at 20Hz before the room adds gain to the response. Expect a 6db increase adding an identical second sub. Anyway...
Assuming the sub is completely sealed with no air leaks...and all power to all equipment is off...
First, you're going to want to run the inuke in Bridge mode. In the inuke remote software (or via front panel) select the Configuration tab and click Bridge. The 390ho has an RMS rating of 800w with a max power handling of 1600w. The inuke in Bridge mode is listed as 1050w. Next click the Filter/Crossover tab. Under High Pass 1 input 20Hz and Linkwitz-Riley as the filter type and 24db as the slope. For Low pass, this depends on how they are integrated with your main speakers, but 200Hz for the Frequency, Butterworth filter type, and 18db slope should suffice.
Go ahead and save your settings in the inuke under the Setup tab.
Adjusting sub eq and phase will really require an acoustic measurement system that Martycool suggested. It would be much easier to see the systems' frequency response as you make adjustments to a filter, phase, eq, gain etc. Of course, learning REW (Room EQ Wizard, measurement software) and how to take proper acoustic measurements will be quite a learning exercise if you're having trouble understanding the inuke manual, but it would be well worth it. The microphone is relatively inexpensive and REW is free and if you have a laptop with usb, you're set.
Second, for the Bridge mode on the amp, you'll need to use a Speakon NL4FC male connector and wire it 1+ 2+ with 12AWG 2-conductor speaker cable. Google "NL4FC wiring" for instruction. If you're building a theater and doing in-wall make sure it's CL2 rated. Connect the speakon to the B output on the inuke and connect the other end to the sub. It really doesn't matter what connector is at the sub end, you can use speakon or banana since it's only 2-conductor cable.
Third, turn on equipment, play some music with the inuke volume down and slowly turn it up.
From here, it's a matter of checking everything from the source to the sub if you encounter problems. Good luck!