Originally Posted by kanzimonson
Man I hate bottle conditioning exactly for reasons like this. Definitely my first recommendation is what people have been mentioning about actually measuring the volume of beer being bottled. That's NOT the recipe size, it's NOT the amount of beer in the primary, it's NOT the amount in the secondary, it's how much is in the bottling bucket. From brewing to bottling I've sometimes lost 3 quarts of beer if I use a low-flocculation yeast and use a secondary for adding flavors/dry hops. You have to adjust for the fact you're bottling less beer.
Furthermore, you also need to account for how much carbonation is currently dissolved in the beer. Just because your carboy is unpressurized doesn't mean there's no CO2 in the beer. Any liquid can hold a certain quantity of CO2, depending on its temperature, but I find this an incredibly frustrating thing to estimate.
For example, let's say you have a beer that ferments at 65*. Then it finishes, but you have a heat spell come through and the beer makes it up to 70*. Because of the higher temps, wouldn't you have less CO2 in solution? How much less? Also, I find that the vigorous activity of racking to a secondary will cause some CO2 to escape the solution, but I don't know how much.
I tried to be so meticulous with temperatures and weighing my ingredients, and I still had problems with low and high carbonation. I finally got the kegging equipment and never looked back.
If you can control those factors though, it can be done properly. I carb all of my beers to style. I've accurately measured and marked my carboys and bottling buckets, I know exactly how much beer will end up in my bottles. I've actually got it down to the bottle now. I'll sanitize 52 and fill 52.
I temperature control my fermenters, so I know exactly what temp my beer is going into the bucket.
I've not had any problems with carbonation. If I want it fizzy, it will be fizzy. If I want a smoother, less effervescent carbonation, no problem. Knowing your temps and volumes of your equipment is a key part of homebrewing.