Chococat has given you quite a bit of good info. Ill add a few thoughts from my own experience.
Yes, some units are better than others. The best ones are near the middle of the park road, where you're above treeline in open tundra. When the weather's good, the vistas and views of the mountain can be jaw-droppingly gorgeous. However, these units are the most popular, and you'll probably have to wait for them. The units out near Wonder Lake are usually open, but the terrain is low-lying muskeg, wet and can be extremely buggy.
Group size can also be a problem. Some of the units are only open to 6 or 8 people per night, and if there are four or more of you, getting all of you into one of those units will be a real problem.
The bear-proof containers are available at the visitor center, and are required for all backcountry campers. As far as I know they're still free, though.
If you can't get into the backcountry there, you can always backpack at Denali State Park (www.dnr.state.ak.us/parks/units/denali1.htm) The Kesugi Ridge hike is wonderful, and also offers great views of Mt. McKinley (on good days).
Hope this helps. I'm in Anchorage, have visited the park about 20 times or so, so if you have more questions, drop me an e-mail at [email protected]- I don't visit this site all that often. Good luck with the plans.

-Tom-