Personally, I like Atlas cars. As stated before, they are a good compromise between quality (very good) and price (again, very good). Micro-Trains is dubbed the "Cadillac" of N scale, and with good reason, they have the best detail and some even have operating parts (sliding doors on boxcars, opening flaps on hoppers, etc) that you just don't see in the other cars, but as the nickname implies, they come with a "luxury" pricetag.
The newer Atlas cars come with Accumate couplers which are compatible with Micro-Trains couplers, though some people complain that they tend to fall apart. While this hasn't happened to me, I can see the merit in the argument. Just be sure when you get Micro-Train trucks to get the low profile wheels, as you mentioned you would be using Atlas Code 55 track.
However, do not overlook Life-Like rolling stock. As with their locomotives, they do have some nicely detailed cars - the cupola caboose comes to mind. You can usually acquire these cars for ludicrously low prices (I got some for $1.99) and the level of detail on them is quite good. You will have to get trucks for them, as they come with Rapido couplers, but if this has already been budgeted, you can get some good deals with LL.
I would avoid Bachmann cars. My friend bought a couple and I'm not convinced about them. They tend to derail (likely due to weight issues) and the detail doesn't seem as good. However, I have limited experience with those cars.
Kato makes decent cars as well, however I do not like how some of the cars and trucks cannot be parted. (The 2-bay hoppers come to mind.) If you get Kato cars, make sure they have knuckle couplers installed.
I only own one set of Athearn cars (the Tri-Rail Bombardier passenger cars) and I must say that I was very impressed by the quality and level of detail in them. I would definitely continue to look into Athearn cars. Not to mention, their road trucks are very cool!
There are countless other makers that I have no experience with. Red Caboose cars look to be high quality, but I can't back that with personal experience. Deluxe Innovations (I think it's called) did not look very good to me.
Enough rambling for me. I haven't been in the hobby long enough to give you better advice in this area, so I just related my experience. So take it as just that - my limited experience.
