There could be a few possible reasons for a mismatch of your Amount in Zoho Books and Amount in Bank.
To know more about Categorising and Matching a bank transaction, refer this document.
Check if there are any duplicate feeds pulled in, and you have categorized the same.
Once all the feeds have been fetched, there may be a case wherein the Amount in Zoho Books fails to match the actual amount available in your bank account. This would be because the balance amount might be attributed to the transactions carried out beyond the 90-day period.
You can record the balance amount within the Banking module. Click on Add Transaction -> Other Deposit. Enter the amount and choose the From Account as Opening Balance Offset.
Now, the amount in Zoho Books will be the same as your bank account.
and GST filing.