That all looks good to me.   I have all of those speakers with the exception of the sub, so I can attest that despite being an "entry level" speaker, they still sound really good.
 
 
 

That receiver is an excellent choice...  I have the Onkyo 646 model so the one you are looking at is just the next step down.  They are nearly identical the 545 just has a little less power and doesn't have DTS:X - which isn't even widely used yet.  Yes you can run it in 5.1 mode (which is what I am doing) and later change it to 7.1.  When you initially set the receiver up you hook up the HDMI-out to your TV and there is an entire setup you have to go through to tell it what kind of speakers you are using and how they are placed.  Then you can also run the microphone setup which will calibrate/tune the EQ for your room.
 
The speakers are also a GREAT choice.  Duckman has the exact ones and I have the newer ones which are almost the same.  My wife and I demoed the Pioneer speakers listed above next to the Polks in the store when I bought them...  NO comparison - the Polks blow them away but sound is subjective and the next person might thing the opposite.  That Klipsch sub should be more than enough - especially for an apartment plus having the tower speakers up front.  I've got the 12" version of it and I have to turn it down sometimes even being in a house.  If you are able to place it in a corner it really makes it louder (they call it corner loading).  Another thing to note is that these Onkyo receivers support 5.2 and 7.2.  So later down the line you can either replace the sub with a bigger one OR add a 2nd sub which is becoming a much more common thing to do.
 
Lastly - you are correct about upgrading to 7.1.  In the future if you want to upgrade from 5.1 to 7.1 you would just need another pair of bookshelf speakers in the rear.

I think I'm going to get that Onkyo Receiver from groupon since its on sale. But it will be a couple of weeks before I get the speakers. Going to start with the Receiver, Sub, Center, and Tower Speakers then get the bookshelf speakers to upgrade to 5.1 later next month. Will post pictures to show the setup.

They just took off an extra $50 on that Onkyo receiver from Groupon.
 
It has good reviews. I Wonder why its on sale. Defective or they just made too many, idk.

Am I the only one that misses the old graphic EQ's?  

LOL. I had a dual 31 band in my studio for a long time. While it was really cool for that "hands on feel" in the end, you can just load in a vst (Plug-in) that does it all on screen and half of it automates for you. I used to have a big old mixing board too...

 
 
Well, not quite that big but again, I can do it all on a 2 foot computer screen now. Saves space and saves me from having to clean all those pots and faders that get gummed up.

Tweaked
The Andrew Jones line of Pioneer speakers are excellent for the money.  That would be my choice.  I would also look at a Marantz Receiver.  I love mine.

For 500$ yes... They are comparable with many 1000$ systems.
There are excellent speakers and for 300-350$ in line with most 500-600$ systems, and off course there are more expensive.
But really no reason to go more than 500$ for Pioneer from picture with some nice 5.1 receiver and sound card as Sound Blaster ZxR.
 
 
 

I don't really miss the old graphic EQ's.  I much prefer today's parametric EQ's.  Much more precise control and more flexibility.

My car's stereo has "cool visuals"
 
Its the most annoying thing ever, but I lost the remote and it shorts if you touch it so I cant change it. Its a little car driving around.

What gauge wire should i get? Been reading that 16 is the way to go.

WackyWRZ

kidcrumb
What gauge wire should i get? Been reading that 16 is the way to go.

16 is fine up to about 50 ft - but if you can get 14AWG for not much more I would recommend it - and 12 is way overkill for that receiver.  Monoprice is a really good source for quality wire.

Agreed.   All of my speaker wire is 14 gauge.  Plus get some banana plugs.  You'll thank me later.
 
But be mindful of the shipping charges.  Sometimes Amazon is cheaper. 

Thanks again guys. On the 30th, Ill put the order in to set up the 3.1
 
Then the month after Ill grab the other two speakers. Will update with pictures. These speakers are overkill for the space I'm in right now, but hopefully they will be with me for a few years.

WackyWRZ
Oh even if you had a house and built a dedicated theater room I would think this setup would do well even for that (at least as a start) - meaning this system should last you for quite a while!
 
Definitely looking forward to pictures and hearing your impressions!
 
Edit: Since you aren't buying for a little bit - keep an eye out.  There are often great deals on higher end Klipsch subwoofers going on.  For instance - with the promo code you can get this speaker from Fry's for $150 (which is $200 off! until 7/23) - http://www.frys.com/product/8231666?site=204premail071716 .  If there is a sale at Fry's when you buy and you need a promo code PM me!

 
I dunno.... Frequency response= 32Hz-120Hz. I think you can do better than that sub. I like Klipsch speakers but you are not going to get a whole lot of bang with these little 10'', small box subs.

Hi!
 
I'm using the LG LHB755W and I'm very happy with it. It comes with wireless rear speakers. If is not a problem to have wired rear speakers, you have more cheaper models from LG.
 
http://www.lg.com/us/home-audio/lg-LHB755W-home-theater-system
 
I use them using the optical in from my linux box, but you can use HDMI if you want. LG has more models with wall mounting speakers, so it's your choice.

They should. I think going Polk is a step in the right direction.
 
Just be careful reading some of these specs... Reading stuff like "Low Frequency Effect x2" and the rating of
"Frequency 26-200 Hz" from a 5 1/4" Woofer is just going to confuse people. That little woofer may hit 26Hz but it's going to be a level so low that you would never hear it or barley feel it. When you hear about settings or features like "Low frequency effect" that's like saying "Emulated 1080P". Usually that is a warning sign. Not to come off like a snob but LG is a great company but I feel they are best sticking with displays and cell phones. Sony is not what it once was but to each their own. Also, for the price range you are looking at, you are not going to hear much of an audible difference in wire gauge.