I think I would buy that Onkyo package that is going for about 450 bucks right now. Then save your left over cash for some serious upgrades later on.
You have the cash for something just above a home theater in a box setup. This leaves you wanting to get stuff separately, but not really with the money to do more than pay for the extra packaging.
Forget it! Just get it all in one box with a halfway decent receiver that will last you a couple of years or more. Then get a kick butt sub with it if you want to later on.
There are some used Velodyne HGS-10 subs available for under 1000 bucks online which will shake your room to the floor - or maybe a Sunfire. My opinion is that if you can't go with the best, but you want the best, then don't waste money on anything less unless you don't have anything at all - then buy the cheapest you can that'll make you happy and start saving your cash.
Have no doubts that the Onkyo when used with a real sub will be far more impressive than the Yamaha with that speaker package. On the other hand, I love Yamaha stuff and with some good speakers and a serious sub, you would be all set as well - but that is out of your price range right now.
