D6 9U Transmission ??

Well, yes and no.
The transmission and steering clutch case each have their own drain plug but at some level the two compartments are tied together to be read by the one dip stick. The winch is separate.

My winch manual is saying it fills up with the final drives and transmission

If this is for the #25 rear double drum winch s/n 9D501-up the winch is separate with its own fill check plug and drain plug and unit is to be filled by removing the breather. What manual are you looking at?
There are variations of fill and level check methods but all are separate. Post your s/n.

Its got a Hydraulic Blade, so CCU is out must be a D6N Winch.

I looked up the lubrication requirements in the D6N Hyster Winch manual and it does imply the oil in the transmission case and final drive compartment is shared but that pertains to the winch itself.
Filling the winch takes about 3-1/2 gallons of oil. The tractor transmission takes 10-1/2 gallons and the tractor final drives do not share that oil.
Also if you check, the winch drive shaft is sealed from the tractor transmission and bevel gear compartment.
Hope you haven't been running the winch dry!!! as it runs constantly as long as the main clutch is engaged.

I looked up the lubrication requirements in the D6N Hyster Winch manual and it does imply the oil in the transmission case and final drive compartment is shared but that pertains to the winch itself.
Filling the winch takes about 3-1/2 gallons of oil. The tractor transmission takes 10-1/2 gallons and the tractor final drives do not share that oil.
Also if you check, the winch drive shaft is sealed from the tractor transmission and bevel gear compartment.
Hope you haven't been running the winch dry!!! as it runs constantly as long as the main clutch is engaged.