A lot of people (like me) use the bottom vents to regulate temperature. Open the vent for a hotter fire, close it partway to lower the temperature. Obviously, this only works when cooking with the lid on, so the fire doesn't get an unregulated amount of oxygen. Even so, I like to leave the top vent fully open and control the fire with the bottom vent. With a full chimney of fully lit charcoal on my 22.5" performer, I can maintain fairly steady temperatures of 300-550 degrees just by manipulating the bottom vents. (almost closed for 250-300, wide open for 550)
It took me several tries to get what you meant about the charcoal bowl being smaller than the grate. I assume you're referring to the way the kettle shape slopes in under the grate.
When I have a big (direct heat) fire going, the charcoal sort of heaps up and blooms outward, so most of the grate does end up with coals under it. While it may seem illogical, the shape of the kettle actually helps the fire burn really efficiently. Cooking with the lid on a Weber kettle creates a convection effect within. Having had some flat-bottomed charcoal grills in the past, I can fully vouch that the shape of a Weber makes for a better, more controllable fire.
Grilling with dual zones (direct and indirect or direct and... less direct?) is a whole different beast, and you really need to have space on the grate to move the meat to different zones. If you expect to have the entire grate covered frequently, it may be worth it to buy two kettle grills and keep each of them less full. If you're using this method, you would typically put the meat directly over the coals for a couple of minutes per side to sear, then move to your indirect (not over the coals) area to cook for several more minutes. Since you have the lid on, the entire enclosed grill maintains a fairly consistent cooking temperature and the meat gets cooked evenly.
