In terms of taxes on invoices, Xero is a little bit different from Quickbooks. In Quickbooks, each invoice has a single tax rate that is applied to each line on the invoice that is marked as taxable/or not taxable.

In Xero, each line item (product) has its own tax rate, which means an invoice with multiple products can have more than one tax rate on a single invoice. This is sometimes a better solution for some customers depending on the services/products they offer.

In Xero, you have to create your own tax rates and apply them correctly to each line item on an invoice, whereas Quickbooks maintains its own list of tax rates and applies them automatically based on your business address and sometimes the delivery address of your customers.

The Quickbooks approach works well for some people, but not for others where the correct tax rate for the state may not be set up etc.
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When an invoice in Xero has one or more payments applied to it, you can't edit the line items (products) on the invoice. In the service industry, where many bookings are pre-booked a year or more in advance, there are very often changes closer to the booking delivery date (such as guest numbers going up or down), when this happens, you either have to apply a credit note to the invoice and create a second invoice (can require lots of calculations on your part) or you have to remove all payments from the invoice to edit it and them record the payments again (this is not always possible depending on when the payments were received.).

Overpayments - If you are a business that uses advance payments/prepayments (or overpayments as they are called in Xero), where the advance payments are held on the balance sheet, and you create the invoice the day after the event, and match the payments against the invoice, this restriction in Xero does not cause a problem as the invoice is not created until after the event.