Add an Upgrade to a building > Add the Abilities in the Army_Bag > Also make sure that Upgrade is linked with the Abilities > Click Upgrade In-Game > If you did it correctly, the Abilities should show up in the Commander Panel when you research the relevant upgrade
This and...
Like the King Tiger call in, the these custom commanders will show up behind the actual commanders. I do not know of way to add a slot to this but there are couple of work around.
1. Disable Commanders. There is a link for there here:
https://www.coh2.org/topic/59835/q-how-do-i-disable-commanders
2. Add in Dummy slots for behind the commanders to add in a 4th+ commander. The Dummy slots can be hidden after a select upgrade. (Does not work too well with British and how they are Programmed.) Then you will have to add an requirement to
All other select abilities so they do not appear when you select other abilities. This is very time consuming and I have done this in the past, generally not worth it. If done properly when the 4th commander selected only those 5 commander abilities will appear, however if the player selected the fourth they still need to select a commander to remove them. There may be a scar work around but I have not really mess with scar.
3. Edit current commanders. In my mod, how I got single abilities changed was this. Example, Storm Doctrines Tactical Movement to Stormtroopers. Changed the requirement for Storm troopers to any for stormtroopers, and all (ambush, plus Heavy AT mines) and changed tactical movement to not require All (ambush, plus Heavy AT mines). Note this technique affects all doctrines so make sure you require 2 to 3 and check the other doctrines with this combo. Use
http://www.stat.coh2.hu/ to help look at all doctrines at once (that is what I did at least.)