My method: on the recipe side you start with some random figure that seems somewhat reasonable, like 70%. Calculate your ingredients for the OG you wish to achieve at a given batch size. Buy your ingredients, and start a session...
Now, the most accurate time to get an efficiency reading (and we're really talking lauter efficiency here which is what homebrewers are usually talking about) is in the kettle - after lautering, but before boiling. The only loss that needs to be taken into account is the deadspace in your lautertun. You have a volume (such as 7 gallons), and you have a gravity reading (such as 1045 pre-boil). Put this into the efficiency calculation in the brew session (make sure to indicate reading taken in kettle and not in fermentor) and see what you efficiency is.
From this number you can start adjusting the efficiency number on the recipe side so that you don't use too little or too much grist. But it's an iterative process and requires several sessions, at least. I've also found grains matter, at least wheat. I get ~78-80% with all barley recipes, and more like 68-72% with wheat based grists.
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