Hi there Nhound,
It's important that all your transactions are entered properly so that your books can be well balanced. QuickBooks Online is a great tool able to help you keep track of sales and expenses so you can see the profit of your company. I can point you in the right direction for assistance with missing transactions.
For help with the missing deposits from Square, I recommend reaching out to the QuickBooks Online support team outside of the Community. They'll be able to view your account with you in a secure setting to provide some assistance with troubleshooting the missing deposits, as well as notify our engineers. You can reach them using these steps:
Schedule a Callback or start a Chat: click (?)Help in the upper right > type and enter "Contact support" into the QB Assistant > click Contact Us > explain your situation > click Let's Talk > choose Get a callback or Start a Chat.
Social Media: Facebook and Twitter
If you have any other questions, feel free to reach out here.
