Welcome to the QuickBooks family, @achildsAmanda.
I can provide clarification about your tax concern in QuickBooks Self-Employed. For tax payments, it's correct to show them under Disallowable expenses on your returns.
Those expenses that belong to the Allowable section will account again in calculating taxes. With that said, tax payments are separated and entered under Disallowable expenses.
In case you need further information, I suggest seeking expert advice from an accounting professional. They'll be able to guide you further and ensure your books are accurate.
Also, please check out the allowable expenses in the Gov.uk website: https://www.gov.uk/expenses-if-youre-self-employed.
For additional reference, I've attached some articles you can use for year-end taxes, as well as tracking sales tax:
Let me know in the comment section below if you have any other questions. Have a great day ahead.