When logging, you go to record and the config files that were uploaded to the AutoCal tell it what information to pull from both the E38 (engine controller) and T42 (transmission controller).
When pulling your existing tune, you use read and do both Read1 E38 and Read2 T42, which is the AutoCal pulling the tables that make up the existing tune from the two separate controllers.
After everything is done there'll be atleast three files (more if you did more than one log) on the AutoCal: a log file using record which will be a .efi file, one file from both the ECM and TCM using read which will be .ctz files.