Often companies offer only a CL per month to the employees who are on probation and they can avail earned leave only when they are confirmed. However, in case they take more than a leave in a month it will be counted as LWP- leave without pay. I think you should follow the same.
You can easily mange leaves of employee if you are using some advance payroll software like
SaralPayroll as it has already a leave management module in the software.