What the poster above me said - look to the far end of the runway, then as you anticipate the wheels touching down, use the rudder pedals to keep everything straight. Doing it this way will place the immediate vicinity into your peripheral vision and you may find you automatically compensate without thinking about it too much. That's what it will eventually become!
You're right to feel concerned about using aileron so close to the ground, but there's nothing inherently wrong with it. There's no golden rule book for landing an aeroplane, it is something you will pick up through practice, be critical of yourself for sure, but don't lose sleep over it.
Flying can be a bit of a black art at times, whether you have 50, 500 or 5,000 hours
