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Basically, the question is asking you which mode you want to try to get to the historical accuracy in the totals.
Using the pre-calculated ratings will load up the value from a file (total_modifiers, I think) and use that to set the total modifiers. It will adjust each year based on what we have set in the files. So if you either like the defaults in those files, or want to set them yourself, you could use that.
The auto-calc runs the calculation based on the rosters, and will generally be more precise. Since it uses the actual rosters and actually sims, it can adjust for lots of factors to get the totals accurate.
You might prefer using the file values, if you are more concerned with being 'close' to the actual values, or don't like the auto-calc and want to set your own. Generally though, if you use the auto-calc, that should get the values in the green zone when you check in the historical accuracy report, and is the best way to get the totals to line up with history and avoid some of the biggest outliers.
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