First off, welcome to audioholics.
Just to let you know, you would be better served by posting the speaker question in the "Loudspeakers & Subwoofers" thread and the receiver question in the "Amps, Pre-Pros, & Receivers" thread. I will however do what I can to help you here.
As far as the Bose, I am not an audiophile like most here are. I have read a lot of poking fun at Bose. Personally, I don't know the exact problem people have with them. They seem to do a decent job at what they are designed for. I guess one problem would be as you suggested. They are too expensive. My dad has the single cube 5.1 system with a Bose center channel added to make it a 6.1 system. I spent half as much for a Jensen 5.1 system, and to me, I don't see the need to spend that much. Unless you just want tiny speakers. Again, like I said, I'm not the audiophile most here are. Maybe somebody will be along to help you further with your speakers.
As far as the receiver, you are right that you can hook your HDMI from the DVD straight to the TV, but if you don't already know, the HDMI also carries your audio signal. So you will have to run a separate cable to the receiver from the DVD player (HDMI, fiber optic, RCA digital, or just left and right RCA's). If you run the HDMI out of the DVD and into a HDMI capable receiver and out to your TV through HDMI, then you can hook all of your other video equipment up to your receiver. By doing this, if you get the right receiver, you can upconvert all of your other video components to a better quality signal. Not to say that it will drastically improve a crappy signal, because they won't. You will just have one connection to make to your TV. Just to let you know, I just bought the Yamaha RX-V1600. It has the HDMI ins and out. I am not using the HDMI yet, but it is there when I do need it. Also, this receiver does not do the upconverting. This is not a priority for me at this point. The Yamaha HTR-5990 and RX-V2600 both do the upconverting. They also were out of my price range. There is a very good review here on this site about the 2600. There are other brands with HDMI capable receivers. I just don't know the model numbers off the top of my head. As far as not knowing how to connect everything, my manual with my receiver has great instructions on the way to hook everything up. With several options on how to connect various components.
If you will repost your questions, in the threads I mentioned, you will receive more advice than you can possibly process.
Just keep in mind, this is your home and if you are happy with what you bought, then be happy and enjoy.