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.
On a related note, the Move File and Move Folder permissions introduced in Enterprise PDM 2015 are unchecked after upgrading from a previous major version.