We had the same problem, and tried many different apps and services. Finally we built our own: www.donorstatements.com. It’s a web app that integrates seamlessly with QuickBooks Online. It can handle dual sales/donation income companies as you mentioned, and also has many other powerful filters to create a batch of statements exactly according to your needs. It will automatically print IRS-compliant statements preformatted for #9 double window mailing envelopes, or our app can automatically email individual statements directly to your donors.