When the full Facilities module (including online account management) is made active for your software package, any invoices will reflect a note for how a person or member of an Organization can pay online.
When creating an invoice, staff can use the Reminder section to add custom notes. Staff can also add additional legal information that would automatically appear on any PDF copies of the Permit Requests. To add or update any legal information, Select System > System Preferences > Select Facilities on the left then scroll to Printed Legal Information > Update as needed > Select Save.
There is also an FAQ section found under System > FAQs where you could add any notes related to Facilities that you want to have displayed for online reference.
There is not a way to customize or add additional automatic messages to the invoice like the Pay Online message.