Which rules and reference PDFs available on the Academy Games website (or wherever) represents the current rules to be used with all games in the series?
For rules there seem to be two candidates: the June 2012 AtB Rules, and the August 2010 "Eastern Front" rules (I assume the former from the date, but the latter is listed as covering all games). For references sheets there also seem to be two plausible candidates: the 2012 summary sheet, and the 2010 summary sheet (again I assume the former, but that's not clear from the company's website).
The June 2012 AtB rules are the most up-to-date and should be used. I believe there are a few things from SoS (like planes) that aren't covered there, so use the "Eastern Front" rules for anything not covered in AtB 2nd Ed.
The 2012 summary sheet would be the summary sheet to use.