In the EPDM Administration tool you can't. You can open the permissions for multiple groups, but can only select a single folder at a time to change. The sub-folders will inherit the changes, but folders at the same level or in different areas of the vault cannot be changed at the same time.
There is a HawkWare product called EPDM Folder Permissions Editor that allows this type of folder permissions editing. It isn't free, but it could save you a great deal of time and effort if you heavily leverage project templates that also apply permissions. It works on both Group and User folder permissions.
If you have any further questions about these steps, feel free to call Hawk Ridge Systems Technical Support at 877.266.4469 (US) or 866.587.6803 (Canada) or email us at email@example.com.