Let's keep calm and we'll get everything sorted out, Angel11-72.
The transactions that are flowing or should be recorded in your register are already the net amounts. However, Square and Uber have processing fees. Hence, we'll also include them to your sales transactions as we create bank deposits. This would help us not to overstate your balances. To know more about what I'm talking, you can browse this article: Record and make Bank Deposits in QuickBooks Online.
For us to help you correct your data, we'd appreciate more details of what is happening. Thanks in advance!