does anybody know whether the whole AE project has to be rendered two times when I use two pass encoding in ME? If not, how does it work with only one rendering pass?
ANY time you use two-pass encoding, AE renders twice. Unless you're doing something weird like a two-hour-long, effects-laden comp, it's not that big a deal.
But let's say you went with the weird option. What do you do? You render ONCE -- to a lossless codec. Then you use Adobe Media encoder on that lossless file to compress it in the media container & codec for delivery. You can do other stuff while AME does its work.