Some are counted at the same time. Orange County, for instance, was releasing the "raw" count of returned absentees for the June 6th election. A "raw" count is the number of absentee envelopes returned each day from the United States Post Office. However, this number will not be the final count since some absentees are returned (as an example) without signatures, valid signatures, or do not contain ballots.
Until the absentees are verified and opened, an "actual" count cannot be determined. This takes place during the final days leading up to the election (not tallied) and in the days following. The "actual" count will be included in the unofficial election results after each absentee ballot has been verified as valid.
http://www.ocvote.com/live/template52.htm
Thanks very much!