Thumpin

I am just getting started on my new HTS. I just purchased the sub-12 and am trying to determine which is the better quality setup...LFE (single cable) or Left and Right pre-outs. The manual shows both configurations but doesn't say which is prefered. I have also searched for a good source online but nothing. I am sure this must be elementary and maybe a stupid question since I can't find an answer. Also, I will be starting off with a Quintet system (until I can afford bigger) paired with it so I need suggestions on crossover settings. Since these are small speakers I know it may be hard to balance the sound. Eventually I will probably move these to complete a 7.1 configuration but since I just got new SXRD 50", new reciever, DVD player, power filter with battery backup and the plethora of cables it is as much as I can do for now. So, please help me make the most of these speakers for now. Your help is greatly appreciated.