Ditto, the pocket is nornal and works itself out. You are doing it the correct way. The key, as stated, is to fill from the bottom until it comes out of the top hole. (I think this is called the gear lube monitor). replace the screw. Continue filling until it starts to enter the bottom of the gear lube resevoir. Then wait a while. It will continue rising and the air pocket will work itself out. you might try raising and lowering the drive once or twice. If you fill up to the max. line, it will most likely overflow very slowly. Once the level stops rising, then top it off. Then wait again, and monitor the level, it will most likely drop again as the last of the air makes it's way out. Then top off and you should be all set.
This is how my Merc mechanic showed me how to do it.