Pre amp to sub hookup, or speaker level?

Ptm,
The direct answer is don't do either. You want to daisy-chain the sub between your speakers and amp or between the pre and amp. That way you use the sub's crossover and filters to strip the (low) frequencies you want it to produce and pass the remaining (high) to the speakers. Otherwise, they both get a redundant full-range signal.

If I have an inferior quality sub, am I degrading the signal by passing it through the sub on its way to the amp? My subwoofer is the lowest quality component in my system.Thanks for the help

Try not to use the high pass filter of your sub.
The method I prefer is to connect your pre-amp out to your sub (line level), use a Y splitter at the pre-amp out and use a ACI line level filter (two version 65hz or 85hz) going to your amp.
In my experience the ACI line level filters are very transparent and your amp is relieved of driving the bass.