Hi Eric,
You have an amazing receiver. (I have it's little brother - a 4400H.)
I'm surprised you are only going to a 5.1 setup but hope some day you'll get to experience all that the 6400 can do. (7.2.4) Anyway, the manual for your receiver gives a good description on speakers placement, but run anything different by the folks here as they can offer good guidance on compromises due to room (or WAF) considerations.
I would try to put your center a little higher (right under the TV) or maybe angle it so the front is directed more towards the listener. You need to connect your "back" speakers, in your case SL & SR -see photo below, to those posts on the rear of the receiver. The ideal is to get the surround speaker placement to resemble the photo as close as possible with the tweeters at Ear Level.
View attachment 27180
View attachment 27180