Relax, These engines are simular to Marine Gen Sets I work on. They too have two fills very simular to yours.
This is prolly what is happening:
The "lower" fill is where all the internal gears are for the cam, inj pump, crank, etc. When you fill there it drains into the sump slower and from the front ( or rear ) only.
Since you have a semi split sump one is filling more than the other, and the less full one is prolly where your dip stick is.
If you fill from the top fill the oil drains down more evenly and is more uniform in the sumps.
And no, filling from the top will not fill up your cylinders:laughing:. Your pistons tops are not exposed to the crank case.
If your still worried, drain both sumps and guestamate the amount of oil.
Then re-fill from the top.