With any change in your swing you will get worse before you get better. You will need to practice the new swing and re-train your muscles so that the new swing is natural. This usually takes about 500 balls or so. Trust what your pro has tought you and things will get better with practice.
As for be square, your clubface should be on a 90* angle to your target line.
There are two theories about ball positions. The first is that long
irons should be played slightly in the front of your stance, moving about a ball width back with each club down to PW. The other theory is that you should play every iron from the centre of your stance. Work with both and find which feels and works best for you.