I'm new to the stereo scene and need a little help with the proper config for subs. I have Polk RT2000p's for my mains which have built in amp'd subs. Both have line in and line out and standard wire connections. My Yamaha v659 has 1 sub out OR the use of the B front speakers for the sub. My guess for the correct config would be to run a male to 2 female splitter off the Yamaha and then connect lines to both sub in's. Is this any different than running 1 cable from the Yamaha sub out to the sub in of the first speaker and then a cable from that speakers sub out to the second sub's in? I'm pretty sure that these beat running standard speaker wire off the B front connections?
What instructions came with the speakers? I would use that configuration first.
Your first proposal, if I understand your intentions correctly, would normally be correct. The usual advantage of speaker level connections with a separate powered subwoofer is a finer control over the crossover point for the transition from subs to main speakers. I'm unfamiliar with your speakers, so, I don't know whether this applies in your case. In any case, I woud try the split sub out arrangement first.