I recommend lengthening the tops. The stock bottoms are long enough, and IMHO you don't need any more than one knot in the bottoms (although I actually have two until the pigtail wears out).
Take a look at the leader lengths that John Barresi uses. The bottoms are relatively long and the top ones are probably twice longer than the bottoms. This is very useful when you begin doing catch and throw. Allows you to grab the leaders way out there instead of the flying line which can cut you quite badly.