The EP600 should be noticeable when you are playing.
1st. Take the cover off the subs and look at the driver when you are playing. is it moving?
You said you are using a high level input. So you are running the speaker wire from your amp to the sub, and then a speaker wire from the sub to the Polk RTia3 bookshelf speakers.
The high level input has a cross over knob at the top that controls the frequency that the sub will kick in. If you have that set to 40hz then you are not likely to hear any sound from the sub and would explain the strain you hear on the Polks when playing bass heavy tracks. Try turning that up to 100 or 120hz. this will offload the bass from the bookshelf speakers and give that to the sub.
You can also look at
http://www.audiocheck.net/audiotests_index.php for some test sound patterns
