7.1 or 5.1

If your seating area is at least a few feet away from the back wall, then consider doing a 7.1 layout, since you'll be able to get meaningful separation between your side speakers and rear speakers. If your seating is at or near the back wall, then stick with a 5.1 layout, since there won't be enough space behind you for the rear speakers.

Whether you buy a 7.1 or 9.1 receiver, you can connect as many speakers as you want, even if you decide to start off with just 2 speakers initially. Also, modern receivers can scale the number of channels in the source material to the number of speakers in your set-up. A 5.1-channel soundtrack can be downmixed for 2 speakers or upmixed for 7.1 speakers, without throwing away or adding anything to the soundtrack.

So buy the receiver that has the features you want. Don't worry about the number of speakers you'll be using.

If you are still in construction, you may as well wire for 9.1 or even 11.1. A couple bucks extra for some speaker wire will go a long way for future proofing. Off topic, but do also consider extra Cat6 runs, you can never have enough.

That IS the main difference. But since 5.1 receivers are typically at the lower end of a company's product line and 7.1/9.1 receivers are at the top end of the product line, the latter means that you get things like: better room correction, additional surround processing choices, more connectivity, greater amplifier power, etc. So it's worth getting those features, even if you never plan on going beyond a 5.1-speaker layout.

I'll also echo what BllDo posted: since you're in the construction phase, this is the best time to run wire for additional speakers. To that end, a couple of quick questions about your set-up. What are your room dimensions (LxW)? And where is your main listening position going to be (i.e., how far from the back wall)?

Monoprice is a great source for cables (and everything else).

For receivers, if you don't mind looking at factory refurbished models, check out Accessories for Less. You can get a Denon 2113 for $399. http://www.accessories4less.com/make-a-store/item/DENAVR2113CI/DENON-AVR-2113CI-7.1ch-Networking-Receiver-w/AirPlay-3D-Ready/1.html

Otherwise a factory new 1713 would fit the bill nicely.

If you look at the line up of AVR's from the major manufacturers, they have only 1 model that is a 5.1 AVR, with many that are 7.1 with increasing bells & whistles for increasing costs. Your best bet would be to go for the 7.1 models that may have options you could utilize now, or in the near future (prior to your next AVR upgrade). List the feeatures you would need now, then research what is available. Also don't forget to call some of the authorized sellers (Electronics Expo, J&R, AVSF store, et al) to get the current price they are selling the unit for... they typicaly sell for less than the price listed on their web page (saving you money, which may give you an opportunity get a better AVR for the same price you have decided you could afford). Best wishes!

That's enough distance from the back wall to give you good rear-vs-side separation in the surround field. Put your side speakers directly to the sides of the listening are (or a few degrees forward) and spread your rear speakers apart on the back wall.

You're going to have rows 6 feet AND 3 feet from the back wall? That's not enough space (3 ft between rows) unless people in the back row have no legs.

Consider placing the front row at 3/5ths of room length, around 10 ft from the front wall. That will give you 6.6 feet of space for the back row. Sitting at any of the 1/3rd or 1/5th divisions of room length will help improve frequency response.

Place all 4 surrounds at least a couple of feet above ear level.

I have two rows of seating in a 7.1 setup and have my side surrounds even with the front rows headrest.