How do I configure the system so that employees are able to submit leave applications even if they have a negative balance?

This feature is available on all PaySpace editions.
Enter an amount in the "do not allow total balance to exceed the following negative amount at any stage:" advanced options field on the applicable leave type, in order to prevent an employee from exceeding the specified negative balance when submitting leave applications.
Navigate > Configuration > Human Resources > Leave Administration > Leave Scheme Parameters > advanced options