You should have the essential functions on the hotas imo. Things that you need setup by clicking in the cockpit should be taken care of before you engage hostiles or enter into enemy territory.
I tried the mouse stick on my X52, I've found it more efficient to use my actual mouse for clicking cockpit buttons (I have it right next to my joystick) and use the mouse stick on the throttle for slew control.
I have found that if you start on the runway you have to make sure the countermeasures and TGP get turned on. Also look at your weapons profiles, paveways need their autolase and lase time configured too as well as Mav EO.