Providing that your crank is within the specifications listed in section 3-78 of the service manual, you will use the crank and case codes to make your initial bearing selection. In the example that you gave, the case code is AAAAA and the crank is BBBBB, you go to the table in the manual and you find that case A and crank B is a "black" bearing set. Your example is easy because they are all black bearings (A-B). In my case, the case code was AABBA and the crank was BAAAB, so starting from left to right you have AB=BLK, AA=GRN, BA=BLK, BA=BLK, AB=BLK. Once you have installed the bearings in the proper locations, make sure you check the clearance with plastigauge. To answer your other question, the codes only apply to the mains. There is another table in section 3-80 for your thrust bearing selection.
That should get you there. I know that there are some other threads that talk about where to run the clearance on the mains for better oiling, so if you find that your clearance is on the high or low side (or outside) of the spec, you can select the correct bearing to give the proper clearance.