A -- Regarding the AP and PR Check Reconciliation File, you must turn on the flag in the AP (AP Setup field # 3 = Y) and PR (PR Setup field # 18 = Y) setup file to get the checks to record in the Check Reconciliation File. Otherwise, there would be no source of AP/PR transactions coming into Bank Book to merge.
Q # 2 -- What does the AR Cash Deposit record merge into Bank Book?
A -- A Bank Book Merge takes transactions out of the AR Distribution File, which relates to the Cash account in Bank Book.
Q # 3 -- How do they get posted to the GL when the Bank Book Reconciliation creates Journal Entries for Interest and Service Fees?
A -- Yes, Bank Book will create General Journal Entries in GL, but you need to take one more step which is to "Post General Journal Transaction" in the GL module.
Q# 4 -- Do we need to Merge GL transactions to Bank Book for related Cash transactions?
A -- No, General Journal Entries will merge into Bank Book automatically as long as the transaction has been posted.