Have two checking accounts, main and secondary. While doing bank reconciliation for the main I found 3 deposits made to the main that should have been made into the secondary. The deposits are in the correct accounts in the general ledger. How do I deal with this?

Just transfer the money from the main account to the secondary one.

Your journal entry will be a credit from one account and a Debit to the other one.

The transfers have been done to the other account in the next month, this wasn't caught until the next month, but the bank is showing the additions in the month being reconciled. What is the best journal entry so my bank to book reconciliations match for the month the errors were made.

If the transfer has already been done and the entry was made, then no other journal entry needs to be made. I would just make a note of the fact on the bank reconciliation statement.