Please share whatever works for you.
I have three counter trays.
One has just the markers. It is pretty full but they fit.
One has the Germans and Austro-Hungarians. They take half a tray each.
One has the Russians - half a tray for those used in the northern scenarios; the other half for those used in the southern scenarios. The campaign-only Russians fit into the northern half of the tray.
The campaign-only Germans and Austro-Hungarians are in ziplock bags - too many to fit into the trays.
The counter sheet sprues (used to mark areas of attachment) are in a separate ziplock bag.
Within each counter tray, the units are organised in the same order they appear on the set up tables (so fortress units and army depots first, with artillery asset units last).
That means when setting up, you can follow down the set up chart and the trays are in a corresponding order.
That system works okay. There are still lots of pieces, and some hunting around but it is manageable.