It is in regards to the player value of the keeper. Overall ratings means that your keeper hold a certain round value 1-30 = 1st rd, 31-60 = 2nd rd and so on. For example a top 30 player say Westbrook will be your 1st rd pick if you keep him. So for a lot of teams the draft won't actually start until your 6th rd pick if you have a good set of 5 keepers. It helps the teams who don't have stars to pick first, like the 76ers.. who don't have a top 30 player.
Bottom drafting means they go to bottom of the draft, i.e. Last picks. The draft would just follow the normal draft order.
Personally I like the overall system as it helps give the lesser teams some talent.
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