Not an instructor and everyone has their own method, but when I'm playing good I stand behind the OB and center the OB and the pocket, while looking at the pocket. At this point the OB is not in focus and I am focusing on the pocket. I continue looking at the pocket to see the way a ball fits with the most room for error. The OB should end up being centered in your vision automatically. You just gotta figure out how to stand for it to center up, ie it looks right. Get it to where you see the exact place the ball needs to go with the most room for error. I quickly look at the OB and almost instantly see the point that puts me into the pocket. Just a quick glance to snatch where to hit it. I keep this place on the OB in mind and focused in my vision. While looking at the OB and keeping my vision on it (think steadycam or how a chicken moves it's head), I walk behind the CB and it kind of magically centers where center ball will hit the point quickly taken on the OB. I just get down without looking at the CB and shoot. The CB is never my focus when I'm shooting good, only when I'm not focused will I find my eyes wandering to the CB.
How do I know where I'm hitting the CB? How do I know what spin and account for deflection? The trick is, I don't. I pick a target for the CB and let my subconscious do it's job on picking english. It sounds directly opposite of what should be, but it works. If I want to miss shape or my shot, the best way to do so is to focus on the CB and where my tip needs to go. It's OK for practicing new shots, but not what I do when competing. The real key is here I must feel what's happening and not think about what needs to happen. If I think about it, I'll end up picking something off and will miss the shot or the leave.
It seems like you would bump the CB, but surprisingly your body knows where the tip of the stick is and you wont bump into it. Like anything it will take a while to burn the new method into your game, but it goes much faster than you would think.
IMO, aiming systems are for use while building your trust and "pool database" in your muscle memory. Once you have that you don't need aiming systems and they serve as more of a distraction than anything. The same goes with kick shots, banks etc. The systems are for use until you can do it without them. When you no longer need the systems, that's when you really start nailing the crazy kicks/banks/etc that make your opponent's jaw drop. If I want to miss a shot, the best way is to use an aiming system rather than hit it where it needs to be hit after actually lining the OB up with the exact part of the pocket that gives the most error room.
Watch some HD matches with a few your favorite pros and pay attention to their eyes when you find one with good camera work. You'll notice different eye patterns, but the common element is how they lock their eyes on the shot once they know it is the correct one.