Is there a way to set a customer preference for emailing transactions to a specific email address, but then set it so that invoices only are emailed to a different email address? Any best practices are greatly appreciated.

NetSuites native emailing functionality is very basic and can only send transactions to the 1 email Your requirement would probably be best as a workflow. Create a custom field on your customer record for A/R Email or Invoicing Email Then create a scheduled workflow to send out invoices using that field when they are created

Thanks so much! This is extremely helpful :)