How do I mark entries as invoiced if I don’t use the Invoicing option?

If you’re only using the project management and time tracking functions of Paymo, but use another software for accounting and invoicing, you should set up your projects as non-billable

If you want to keep track manually of billed & unbilled time, you can set up billable projects, then mark time entries as invoiced by going to Timesheets → Agenda view → Select a time interval, check the time entries → Mark as invoiced button.