I'll outline some steps you can take to troubleshoot the problem with manual uploads, Cath.
To ensure I address your concerns effectively, could you clarify if you meant manually uploading bank transactions? If so, did you encounter any error messages? Knowing this will help me provide a more tailored answer.
In the meantime, make sure that you follow the specific formatting rules to avoid errors. You can refer to this article for further details. Please know that although this resource is intended for customers using QuickBooks Online or Sole trader, the same principles apply to QuickBooks Self-Employed(QBSE) : Prepare your CSV file for bank upload to QuickBooks.