Practice by setting up square to your target line, then close your eyes before stroking, the object being to settle the direction issue at address. If you are still thinking direction just prior to stroking, you are likely indecisive, which is the cause of many wayward putts. Comfort zone habits are hard to break. Just make up your mind you are going to do so by taking straightshooters advice and hit a ton of practice putts with whichever "squaring" method you choose. My bet is it won't take as long to overcome as originally feared.