Scriptfixer, the answer is yes...and no. The young officer arrives fresh out of flight school, and even if he arrives with an Aircraft Commander qualification, his Company Commander is not going to send him out in command of an aircraft straight away. He will fly with an experienced CW, WO or commisioned pilot to learn about being an Army pilot, which is a lot different than flight school.
As he gains experience he will be given simple missions as the Aircraft Commander, again building up experience until he becomes fully Combat Ready.
As to whether the Aircraft Commander is the same as pilot in command, then not necessarily. If you mean the pilot in command is the one physically flying then no, the Aircraft Commander could be sat next to him reading the map. Then again, as they are both pilots, then they could be one in the same.
The relationship between the new LT and the old and bold CWs is a delicate thing. The new LT arrives greener than a green thing that's just been painted green. The "old" Chief has probably been there, done that, and(in the US Army!) probably got the medal. He will say "Yes Sir", "No Sir" and follow the LT more out of curiosity than anything else. If the LT has any sense, he will realise this and listen and learn, thereby making his life a whole lot easier. Sadly, some don't