Good day, @khamr.
I'd like to get you pointed in the right direction to help fix this issue with the posting of your bank transactions.
The posting of the transactions in QuickBooks Online depends on their mapping of where the entries are coming from.
To verify the mapping of your bank entries, I recommend reaching out to the Square support team. They'll be able to check the settings of your bank transactions, so it will be posted in the right account once downloaded in QuickBooks Online.
Once it will be posted accurately, you can now categorize and match them in QBO so you can have a smooth reconciliation. In doing this, you can always use this link as your guide: Learn how to review downloaded bank and credit card transactions and put them in the correct account.... The said link also provides a video tutorial about the process.
Please keep me updated on how it goes by leaving a reply below. I'll make sure you're taken care of. Have a good one!