You can chnage the end date while scheduling the report. if the report is already scheduled, you can reschedule the report with new end date.
What ever you see in the CMC and Audit universe should macth. It should not eb any diffrerences.
Best Practices:
Schedule the long running reports in off peak hours.
Set the limits on the number of instances depending on your business requirements
Setup custom calendar if deafults does not meet your requirements. So you can apply the custom calendar for the required reports