Setting it up
At onboarding, or later in settings, say whether you collect sales tax and give your registration number and default rate.
On an invoice
The default rate is filled in on each line and is editable. Lines that are not taxable get zero — that is per line rather than per invoice, because most businesses have both.
Tax charged posts to a liability account, not to revenue. It was never your money; you are holding it for the state until you file.
Filing
Reports → Sales Tax shows what was collected for a period, which is the figure you file. The liability account shows what is still sitting there waiting to be paid over.
If the rate on new invoices is wrong
It comes from the company default. Change it in settings and new invoices pick it up; invoices already sent keep the rate they were sent with, which is correct — you cannot retroactively charge somebody more tax.