Invoices go to general sales by default but you can change the nominal code for an individual line by clicking the little cog wheel icon in the line description box.
And yes, a single line invoice would be fine if you're only selling a gift voucher in that transaction, I was thinking from my shop point of view where I might be selling a few pounds worth of vouchers in amongst a few hundred other (general) sales and entering them all on one invoice - you need different lines for different nominals.