at first, i make them about the same size. if they are quite big anyway due to the map, i sometimes keep them without checking (not the best way). so to see on jungle raid. but if i don't have such huge mainbases [where exact size doesn't really matter], i work like this:
i make them all about the same size. then place as many barracks as possible into the 1st main and see how many they are. go on for the 2nd, 3rd, and 4th mainbase. if the count is below the number of the 1st main (with the size you want to have), add some space. if above, cut a bit out.
so easy.
i usually add some more space if the main is located in a uncomfortable position, where placing gates and factories is more difficult. like on 9h position of jungle raid: the base exit is on top, units spawning below each building, so you'll need some more space...putting everything to the upper edge just doesn't work so well.
place the same exact shape via buildings in each, reform each to fit the buildings. how do you think stimey rebuilt from scratch start locs of LT for "tradition", reversed them, etc.?