ACA 1094C\1095C File Transmission Process

I have some questions regarding Part 2 ACA Processing and need some clarification.  Here are my questions:

1.  I understand the whole one transmission/multiple submissions process.  The client I am at has two EINs we processed for 1095C with one AIR ID.  When I process the 1094C Transmittal Workfile Build (R08121A) I get two records under one AIR ID based on Tax ID.  This is correct.  The 1095C Forms Count field is populated and ties back to the number of 1095Cs we produced and all the months for column B and C are populated for each EIN.  When I go into the Select 1094/1095Cs For Transmission I have two files with the Authoritative  Transmittal Flag checked for