When it comes to invoices, you can either create a bank transaction (using the ‘Input New Transaction’) and then tag it to an invoice, or you can use the “Log Payment” option when viewing the invoice. The end result is the same.
The difference would be how you work. If you upload a bank statement or have a bank feed set up, then there’s no need to do either as the transactions would have been created for you.
I would suggest giving them all a go if you get the chance, and seeing how you work best.