I'll usually limp with AQ early (unless I'm in late position and it's unopened, but I'll usually fold AJ in early position (unless it's suited and the table is passive, in which case I'll probably limp), but will occasionally raise with it in late position if I can open. I try not to get too deep with AJ though, unless the blinds are big, in which case I will at times risk my stack with it (depending on the situation.) However, I would suggest not betting the flop when you miss with AQ or AK unless you raised coming in and are now making a continuation bet. And make sure you size your bet well when you do this (avoid better either too much or too little in this spot: about half to two-thirds of the pot is usually about right here, depending on you table.)
Thanks for the advise, I'll incorporate some of your adjustments in my next game and see how I get on.