Sorry to see you are not finding the invoice templates useful. If you haven't checked out already, you can import your own invoice design using our 'Import Style' feature - to activate this on your account, go to the Cog Wheel > QuickBooks Labs > Toggle on Import Style. You will then find the new option to import your own template by going to Custom Form Styles > New Style drop-down > Import Style.
You can create invoces seperately through Wave however as the systems do not integrate you would still need to enter your sales manually, either by raising invoices/sales receipts or adding sales directly from banking.