I'm a Family Physician in Maine. We manually input immunization info into our state registry called IMMPACT2. Same experience as you, lot#'s, etc. Yes a hassle but we record it only here in IMMPACT...not in AC. However we record adult immunizations in AC.
While there is no interface between AC and State of Maine, we still uploaded our adult immunization data to the Maine IMMPACT2 program. For the Meaningful Use measure on immunizations, we used the export feature in AC to create a .txt file containing our immunization database information, which is in HL7 format.
The State of Maine gave us an access code to their webportal in which we copied and pasted the export .txt file from AC. It was quite simple. However I asked AC Guardian Support to walk me through. They have a woman at AC Guardian Support whose job is to answer MU questions. I forget her name but she was extremely helpful. If you asked for the MU support person at AC, they will know who you are asking for.
If you are going to attempt to satisfy the Meaningful Use measures, I would strongly recommend consulting with her if you need to produce the export file to meet MU measures. Furthermore, I would strongly suggest talking to your State Immunization people to find out how to upload immunization database information to their webportal (if they have one that will accept HL7 format, by the way this is the most common format for data exchange). Even if you are not going to attempt attestation for MU, you may still find it useful to learn how to export the data for uploading to your state registry. Good luck!