Hi!
As far as I know there is no mod to change the Luftwaffe markings.
The markings are bound to the unit you choose for the planes. Bombers have numbers and letters (A3+EH), whilst fighters use letters only (3+-), often in combination with a tactical sign like the chevron.
Here you can find more information:
http://www.warbirdsresourcegroup.org/LRG/markings.html; pictures you'll get by google search.
Stationary aircraft gets their markings from the game which is sometimes funny. There are no fighters with a tactical number like 86. To avoid this, you can create a taxi to takeoff waypoint and assign that to a spawnpoint (generic spawnpoint plane). Give the object the correct number by choosing the unit. Then give them a starttime after missions end and they will sit there as eyecandy with correct markings until you come home. However the game provides something like "Stab III/JG 26" and you can assign a complete Gruppe (up to 64 planes) to it - in real life Stab units consisted of 4 - 6 planes featuring special markings ( <| + - ). I'd really appreciate a mod for assigning those special markings to a chosen plane...
If you want those special markings, you'll need a skin for this. Even though there are tons of them, the historical correctness is often not given, as paint scemes differ, too. So you might get a skin with the Kommodore markings, but the paint sceme is for the desert. Makes no sense up in Norway.
Hope it helped a bit.
Have a nice day,
BigMug