Use the level at rest. If it's off balance at rest, it's sure gonna be noticeable when you're running.
With that said, I've found my Allisons have ran best loaded a little heavier on the left side. Just a little, like 20-30 lbs more. If they're perfectly level, they run perfectly level until the upper 80s to 90. Past that, they start lifting the left side a little. I always load a little heavy on the left side now. That way when really strung out, it's perfect. But for learning, level at rest is probably best.