3.1 (or 2.1) channel setup for under $1500?

[415bluray]

I can use some help with deciding receiver, speaker, sub choices for my living room.

I'm leaning towards:

Receiver: Yamaha RXV663. Can this receiver be setup for 3.1 or 2.1 channel? Is it a waste to get this receiver to run 3.1? I wish it had 3 HDMI inputs though.

Sub: Klipsch Sub-10 or Sub-12.

Speakers: open to suggestion here.

Thanks!