Create 2 new items in quickbooks. One will be NSF check. use your operating account as the account like checking or whatever you name your operating account you deposit your customers money into.
Other will be "Bad Check Charge" Give that item a normal charge (like 25 bucks) so by clicking, it will automatically put the correct charge on the invoice. On the first one, leave the amount at zero so you can put in the amount of the bounced check.
Make sure if you charge sales tax, each item should be non tax, because you already taxed them on the original amount.