I have t-amp based 2.1 systems on two computers. One of them uses the Dayton Sub-80 (the other uses SVS SB12+).
The Dayton sub-80 rca outputs are just pass through - no high pass filter.
However, the speaker level outputs are high pass filtered.
Here is how I set up the sub-80 system (actually both are set up this way).
Computer > DAC > t-amp > sub > bookshelves.
You could leave out the DAC and use the computers built in one.
This way the t-amp volume controls volume to both sub and bookshelf speakers, and the sub provides a high pass output to the speakers.
On my sub-80 system I found setting the phase switch to 180, the frequency to 1/2 on the dial, and the volume at about 1/4 worked well. YMMV. I set mine up using roomeqwizard for measurements, if you are doing it by ear you might want to use my settings as a starting point.
Edit: and I put a piece of foam in both ports of the sub-80. It measured and sounded better to me that way. Again YMMV
Everything I say here is my opinion. It is not my employers opinion, it is not my wife's opinion, it is not my neighbors opinion, it is My Opinion.