Hi Phelec
On the Community Forum we encourage users to provide assistance and advice, as such, you won't always receive an immediate reply from an MYOB Moderator. If you require immediate assistance we recommend contacting our phone or Live Chat teams.
If you would prefer not to use Employee Self-onboarding go to Cards>>Employee tab>>New>>when the Employee Self-Onboarding window opens click Skip and manually enter the employee details.
If you send the Self-onboarding email an employee card is automatically created. However, pay runs should only be processed for the employee cards selected in Process payroll. So that I can look into this for you can you send me screenshots of the employee cards and pay transactions in a private message.