Problem: How to reflect money on the account "Cash in Transit" ?

Solution: You will need to create a couple of documents 

1.  To record the receipt of money to the account Cash in Transit, please create Cash Receipt document , go to Money module - Cash Receipt.  Press drop-down list In Cash Account filed , in the opened box create Cash Account - Cash in Transit and pick it .

The received money will be reflected in the debit side of GL account Cash in Transit

2. To register the funds received to your bank accounts , create Money Transfer document, go to Money module - Service Tools - Money Transfer. In the field Transfer From  select Cash Account - Cash in Transit, in the field Transfer To select the Bank Account.