Speaker wires should have some type of indicator to differentiate + from -. It could be something very subtle. Sometimes one side has a couple of ribs running along the side of the outer insulation, while the other side is smooth. Sometimes one (actual) wire is copper colored while the other is silver colored. Sometimes there are actual "+" and "-" markings on he outside. Probably other ways I have missed. But almost always there is some type of identifier, even on common lampcord (which is often used for speaker wire).
I am not familiar with those Pioneers. But it is very possible the Pioneers are more efficient (i.e. louder with a given amount of power) than the AR's.
Again, multiple questions being discussed:
1) something wrong with receiver?
2) bass issues with AR's?
3) cutting out with AR's?
4) AR's not as loud as Pioneers?
1>>> test with Pioneers, if OK, move left speaker to right side (meaning the right speaker output on the receiver, don't have to physically move the speakers) and vis versa. OK still? Probably not an amp issue.
IF you are really cranking the volume knob when playing the AR's then possibly the amp is going into some type of thermal protection, I don't know...
2>>> do listening test with AR's as suggested by onemug (and test same way with Pioneers which are known to be good, just to get a feel for what the differerence in bass output should be when doing this test)
3>>> be aware that cutting out could be whole speaker, just mid, just tweeter, even just woofer if wiring inside is really messed up. You need to identify the problem better. After you do, switch left speaker to right side and vis versa, as above, and test again
4>>> I found this:
http://audio-database.com/PIONEER-EXCLUSIVE/speaker/cs-100-e.html, which states that the eficiency of the CS-100 is 97db. This is significantly more efficient than MOST home audio speakers. So yeah, I would expect the Pioneers to be louder than the AR's for given volume setting. Also, if you receiver is only 35W, it is probably not going to do justice to the AR's, which (if healthy) should be very nice sounding speakers.