Why is my bank balance incorrect?

An incorrect bank balance happens because the data hasn’t been reconciled to the bank correctly.  It is up to you to check that the opening balance is correct and that the bank balance is correct after each bank statement import (or after entering any transactions manually).

How do I handle GST paid to customs?

You should enter any GST paid to customs as a transaction in the cashbook with a GST rate of 100%.  It doesn’t matter whether you enter this as one line in the cashbook, or whether it’s part of a “split” transaction.