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.

Is your sub passive or powered? If passive, you MUST provide amplification and run speaker level to it, but don't just bug off the same terminals as your main speakers. You'll need another amp and y-connect the pre to both amps. If powered probably the best way is to run line level to the sub, adjust the crossover/filter appropriately, and return (adjusted) line level to your amp. If this makes no sense, keep posting and we'll get into more detail.