I think it is simpler to run through it systematically and use some known stock for alignment. Different alignment bars sell for pretty cheap.
A. Level the bed. Even after level there are things that could keep you from cutting straight. Saddle wear, tool deflection, headstock alignment, tailstock alignment. There may be only so much you can do. You can level at the feet, but the bed may have a localized bow or bend in between.
B. Make sure the bed is straight. If there is wear on the faces of the bed, the carriage may not run true. Fortunately, all the flat surfaces on an Atlas are easy to check.
C. Align the headstock using an alignment bar with a Morse taper in the headstock. Instead of cutting, this uses an indicator. This will eliminate any toolpost or carriage deflection. In fact, you can check it straight from the bed with a indicator stand and take the whole carriage out of the equation. An advantage of the flat ways. Likewise, the Morse taper will ignore the chuck. It needs to be checked in both axis.
D. Align the tailstock using an alignment tool between centers. Most of the Morse taper bars can also be used between centers, and they do sell longer bars for use exclusively between centers. Also good to check the tailstock ram and make sure it is running parallel and that the whole thing isn't cocked off at an angle. A Morse taper test bar is good for this as well.
E. Cut a test bar and see how it all measures.
Right now, I've got my bed sitting on an old unused pool table with my Grade A 24" surface plate leveled under it. So I've got a good reference plane to check all this. I'm working on the bed in its 'relaxed' state to make sure there is as little twist and bend as I scrape it out.