If transactions or funds are made outside of the system you will still be able to record them in your accounting sheets in order to have an updated balance view. To do so, you will need to make a journal entry.
From the Accounting-> Accounts page, click on the three dot menu near the top left and choose New Journal Entry. This will bring open the New Journal Entry lightbox.
In the Description field you can add in any notes about this entry.
In the Company drop down menu select the company you want the funds to appear under.
Once the Company is selected, in the Account section select which account you will want the funds to be entered into and which will be taken out of.
Finally, enter the amounts that each account will be credited and debited.
Please note, each Journal Entry will need both a credit and a debit entry.
When done click the Save button.