I derive my armies organization somewhat from real life ones. I particularly like this site (http://niehorster.orbat.com/index.htm) and this (http://www.axishistory.com/index.php?id=30) for reference.
Also I try to maintain 3-4 divisions/corps, 3-4 corps/armee, 3-4 armees/armeegruppen.
When a corps gets only panzer/motorized divisons, I rename it to panzerkorps, keeping the numbering, or gebirgskorps when contains only mountain divisions.
All my air units I keep under an Army Group named Luftwaffe, since I dont like handing units to the AI I can keep them under one theater. Makes it easy to get the numbering right and finding them. I keep fighter, bomber and CAS aircraft separated in groups - JG (Jagdgeschwader) for fighters, KG (Kampfgeschwader) for tac bombers, SG (Schlachtgeschwader) for CAS and so on. I dont know how Im going to organize them if I build too many, wish air and sea units had the same hierarchy as ground ones.
In the same manner, I keep all naval units under an Army Group named Kriegsmarine. I spread all destroyers, light cruisers and some heavy ships in several Kriegsflotte, but submarines I keep in separated Ubootsflotte with 2 flottille each.
this is exactly how i organize my forces. i rename all new incoming infantry divisions and brigades such as "Infanterie-Regiment 132". now that i come to think of it, the game refers to the small units that compose a division as brigades but isn't the current level in most militarys regiments as suggested by the default german military names? i thought a brigade was a larger force than a regiment but anyways.
also how exactly how do compose ur panzerkorps. that has been the subject of much consideration for me as i want to keep it realistic and not just load 1 panzerkorps with all my tanks and mech/mot. i thought it might be wise to include infantry early on and later straight motorized divisions as panzergrenadiers (i think motorized can be, not just restricted to mechanized divisions) into the panzerkorps so i am able to have more panzerkorps and spread out my armor more evenly. maybe as follows:
I.Panzerkorps
Panzer-Division 5
-Panzer-Regiment 15 (Armour)
-Panzergrenadier-Regiment 26 (mot/mech)
-Panzergrenadier-Regiment 32 (mot/mech)
now Repeat 2 more times and then add a straight mech or motorized div. of panzer grenadiers to beef up the panzerkorps. having only 1 armour and 2 infantry style regiments is consistant with a real panzer division and really allows u to have more panzerdivisions cheaper
what would u clasify as a panzerarmee? obviously most panzerkorps were integreated into regular armee's such as the 9th armee of Paulus that was caught in Stalingrad. what criteria would u need to have a panzerarmee and how much infantry would u include bcuz i doubt u could make an entire armee out of armour.
just lookin for some neat suggestions
o and i like ur system with giving the navy and air force their own HQ's but do u assign an army commander to those HQ's?