I was quite happy with the lovely unit counters and lovely map in Thunder In The East. Not so happy with how the profusion of generic fort and supply markers made it all look during play. Yeesh, was the encirclement of Moscow a mess! How about selling faction-specific-colored markers for supply and forts, making the lines of engagement both more attractive, and easier to keep sorted out?
Also, I wouldn't mind more brightly colored timer markers. The eyebrow shape is fine, but these tired 66-year-old-eyes just aren't what they used to be. No numbers needed, just red-backed-orange, yellow-backed-green, and blue-backed-purple (if 5/6 is necessary).
Jay is right, Barbarossa is "rush hour" for out of supply markers, and the Improved position markers have greatly diminished in the rules with errata. I hope you're using the v1.1 rules book.
For the countdowns, maybe a few red or other colored d6 that you set on the map. Again those summer months are the busy times.
Most of my play was on Vassal and Ken has spoiled us with his modules.
Each unit can have unsupplied or Isolated turned on as part of the unit, so it moves too.
The Improved Positions in The Middle Sea are a different color and we usually use one color for each side. Here is a file to copy:
July and August 1941 are the worst for the marking of supply status. It is less of a worry, most of the time.