I only use the bottom grate when necessary for capacity reasons. Otherwise, I always use the top grate.
There can be differences in cooker temperature between top and bottom racks. The bottom might be the same temp or cooler than the top if you're using water, and sometimes it might be hotter for a while if the pan is empty and it's radiating a lot of heat upwards. You'll want to monitor internal temp/doneness of meat on each grate separately to account for these differences. You may decide to rotate meat between top and bottom. I'm lazy and don't usually do that. I just cook until each is done, and if one gets done before the other, I remove it and hold it at temp in a cooler until the other is done. Often, what's on top finishes first, and sometimes I'll move what's on the bottom to the top at that point.
You can cook anything on the bottom, but most people will put chicken on the bottom and other meat on top. Or brisket on the bottom and pork butts on top as sort of a basting method. Or beans on the bottom to catch drippings from pork butt on top. The only time I can think of where you cook only on the bottom is when cooking a really big turkey on a vertical roasting rack.
FWIW , I cooked 4 big racks of spareribs on my WSM 18 , and I cooked 2 on the top and 2 on the bottom which I had not done before. They all came out good , but I did notice that the ends of the bones of the bottom rack pair were noticeably charred and the meat was a tad bit dry in thinner areas of those racks. If I do that again I will think about taking off the bottom stuff a wee bit sooner than the top. Or rotating as Chris mentioned.