The game automatically calculates the modifiers needed to produce the proper historical ratios of everything. Just let it do its job. It is designed to be hands-off.
The engine totals are what the game references when it calculates results HR, BB, 2B, etc. These ratios are only approximate and only represent the year of import. For subsequent seasons
OOTP uses the modifiers to get the correct ratios according to history.
If you were to look at league batting average across say a 10-yr span you'd find that
OOTP is beter than 99% on target with historical batting averages. If you look at 100 years worth of data we're talking about 99.98% accuracy with each season weighted equally.
Just turn on the modifiers and play.
I wouldn't be to concerned with minor league stats with historicals. All the players in historicals are major leaguers anyway.