My first few batches of beer have come out quite undercarbonated. I believe because I've been quite cautious about how far I fill my bottles up. This comment backs up my theory.
How can I determine the maximum level to fill my bottles? Is it related to desired CO2 volumes or should I leave CO2 decisions up to priming sugar?
For a 12-oz bottle, I fill it all the way to the top with the bottling wand. The amount of liquid displaced when I pull out the wand is about 2 inches from the top. For larger 22-oz bottles, I fill it a little less, but still keep approximately 2 inches of head space from the top. I've never had a problem with the lids blowing off or low carbonation. Best of luck!
The space in the bottle is important, but don't forget about your priming sugar amounts and bottling temps. If you find your beer is undercarbed, try to rotate the bottles, swirl them gently while they are upside down and raise the ambient temperature up. You'll see better results.
I fill mine up somewhere between just below the flange to overflowing, and then remove the bottling wand or beer gun (keep the wand or gun touching the bottom of the bottle for the entire fill). I've found that this leaves pretty much the same amount of headspace as commercial breweries leave. I do this for all sizes of bottles that I fill.
The only times I have had problems with carbonation were from misreading the nomograph in "How To Brew", and not getting enough sugar in the bottling bucket.
If you aren't getting enough carbonation you probably aren't using the appropriate amount of priming sugar. Most ingredient kits come with a standard size bag, but this isn't always the right amount to use.
I suggest using a priming sugar calculator. This one is great: http://www.tastybrew.com/calculators/priming.html
