Must admit i use the same - except when i am bored or docking re-fueler to the station and just use mechjeb . But the first thing i found is getting the RCS in the correct position - if the craft is to big for 1 set of thrusters - do 2 sets - equal distance from the COM to help balance it out. The final thing is to make sure the craft is in LOCKED visual mode - this means that up is up and down is down etc