John,
If you delete an invoice from Method it will also delete the invoice from QuickBooks, you don't need to go into QuickBooks to delete it separately. If for some reason the invoice can't be deleted it will show up in Method under QuickBooks > Resolve Conflicts.
-Michael
Michael Melo
Product Manager
Method Integration Inc.
Website: http://www.method.me
LinkedIn: http://www.linkedin.com/in/MichaelMelo