Since ACE 1.6 RC1, Configuration is now done mostly in ingame ACE Settings Dialog, press Escape during a mission and select ACE Settings.

But to persist the settings, the external ACE Clippi tool needs to be used.

The Clippi tool does only two jobs, it listens to the clipboard and reacts when the ingame "Save" button
was pressed in the ACE Options dialog and saves the settings to the settings.ace file in userconfig\ace

(it doesn't interfere with other clipboard operations).
The second job is to change the remaining ace_clientside_config.hpp settings.

To upgrade to the new system;
Simply delete the old files in your ArmA2/oa\userconfig\ace folder.
Then extract the userconfig.tar file in @ACE\store (with 7z/rar) and move the files to userconfig\ace.
Run ACE_Clippi (Might have to "Run as Administrator") and change the remaining 5 ace_clientside_config.hpp settings at "Change manual options", that's it.

Don't close the Clippi tool just leave it running when you start OA with ACE.
It takes care of saving your changes that you make in the ACE Settings dialog to the settings.ace file.

If everything goes well you don't have to update your userconfig\ace folder in the future.