At least an inch of the short tube. Usually you would want even spacing. Say you have 9" of uptravel from ride height. The first tube would be 3" above the piston and the second would be 6" up. Unless you're buying custom shocks, you're stuck with the standard setup.
The problem isn’t the spacing on the bypass tubes for longer shocks, the problem is the lack of tubes. Add some compression and rebound trim tubes to your shocks and youll be amazed at the additional comfort you gain. Take a look at the tube layouts on the big shocks and you’ll see some with a small 1” bump zone. However they have 4-6 tubes that shrink in lengths and diameters as they get closer to the bump zone which effectively reduces flow and makes a much smoother damping curve. I’d rather have 5-6 zones that transition smoothly vs 3 zones with harsh transitions