So, to help you a bit with your groups...
(Me isnt as great in PHP like you or even Master Klemen

,so just check for validity.)
->
http://evilcity.net/img/admin.zip
db.sql is for remove old stuff and creating the new table (change prefix and engine to the one you use).
common.inc.php is the "new" features array, just better organized

manage_groups.php is just a customized "manage_permission_templates.php"
manage_users.php and profile_functions.inc.php for assigning users to groups (and removing the direct-assign of permissions)
There are lots of "ToDo" marks in the code, just search for them

like:
* change permission check in manage_groups.php
* change some table columns in code and change permission to edit templates to edit groups
* change various hesklang[]
* edit manage_users.php to save new/edited users with the new group element instead of the perm_template (only displaying yet)
(and remove the categories and privileges from the query)
* edit hesk code to reflect the groups and their permissions instead of user permissions
Thanks.
/* edit
As for creating/editing users, me would check if there assigned the admin group (id: 1) and if yes set "isadmin = 1" else set "isadmin= 0".
*/