The problem with trainer balls is that they're only as good as their setup. In other words, if they're not set up with the dot really representing center ball, and you hit the dot, you're not hitting center ball, regardless of chalk marks.
One trick I've found is to use either the top of the CB or the bottom of the CB as a reference. Think about it this way: how do you find the vertical axis of the CB? Answer: draw a line from top dead center to bottom dead center. When I play with draw, and this happens automatically now, I line up my cuetip at the bottom of the CB, which must be on the line of the vertical axis, then just raise my tip straight up to my desired contact point on the CB. This means I'm still hitting low to get the backspin, and I'm still on the vertical axis, which avoids sidespin. As long as you're on that vertical axis, sidespin can't be the culprit for your missing straight-in shots. Contrary to what another poster said, I think it's best to avoid sidespin on long straight-in shots. More variables become introduced when using sidespin, complicating the shot more than it needs to be.
Another possible issue concerning straight-in shots is visualization. Some people try to focus on the center of the OB. Some people look at the pocket. Some people look at light-reflection. Personally, I don't like ANY of these methods. For the first, it's very difficult to visualize dead center. Hold up a sheet of paper and point your finger at the center of the page. Mark that point with a pen. Find the actual center of the page with a straightedge. The human eye almost always fails this test. For the second, looking at the pocket just doesn't sound like a good idea to me. Light reflection also doesn't sound good to me, since lighting varies from room to room, table to table. Personally, what I do is focus on the very top of the OB. The very top of the OB must be on the vertical axis, which means it's the same as the center of the OB. I've tried to focus on the point where the OB touches the table, but sometimes this is difficult to discern since there's usually a shadow under the ball. Finding TDC (top dead center) on the OB is what works for me.
Finally, a good, solid stroke with a defined follow-through towards your point of reference (for me, TDC on the OB) should deliver the CB to the proper contact point on the OB. If you pause on the finish (and you should), take a look at where your tip is pointing. If it's up, down, left, or right of your aiming line, you need to make some adjustments. Your stroke may *seem* to be straight at address, but if upon follow through your tip isn't along the aiming line, you're not delivering the CB to the proper contact point.
Hope this is food for thought,
-djb