Heh, so no towers in front
Ack, my cable provider sucks today and I'm having trouble getting to most of the sites I want to. So, from memory
I think I'll recommend NHT SuperZero 2.1's for you. www.nhthifi.com Can't access it right now but I believe they are on sale right now for ~$80-90ea. These are excellent desktop speakers and they do pretty good in a smaller HT environment too. You'll definitely need to run a sub with them though since they only reach down to 85hz.
So, running into your budget there, I take it $350 is about what you can spend now which means if you want, you could get the front three and use your logitech sub for now giving you time to save up for one. The SuperZero's and SuperOne's tend to have b stock in there clearance section for good deals so don't worry about getting the rears right away, you can get by with using the Logitech there as well. If you don't mind spending a bit more you could get all 5 now and you can call them up and see if you can get a better deal if you do that, they're a good company to work with and sometimes things like that happen and it doesn't hurt any to give a call, maybe they'll give you a really good deal on some b stock.
For the sub, the one I'd like to suggest is out of stock, it's the Mordaunt Short Aviano 7. The couple of places where it's sold that I know of and their website say out of stock (at least as of a couple of days ago). The reason for this choice, one it's a solid performer at it's price point, but also comes with a variable notch filter. The filter tends to be useful in a desktop situation as the sub is usually placed in a confined area, be it under a desk or between the desk and wall. Because of that there's usually a small frequency range where it just resonates out of control and the filter helps tone it down. Audyssey on the Onkyo will do that too, but usually the less work Audyssey needs to do the better. I don't remember the price of it off hand, but I think it's around $280.
But there are other subs to look at too though it'll depend on size restrictions and budget. *
*For fun I'd suggest getting a couple of Orbit Shifters from JTR. Probably won't shift Earth's orbit, but maybe you can get them to shift your office across the street