If you look at the pics above, you will see two pieces of blue painter's tape. One is on the hub and one is on the fender. Typically, you stuff the tire into the fender, measure, then lift the other side, so the first tire will drop down as far as it can, then measure again.
At any point, top of tire, hub or bottom of tire, the overall "wheel travel" is the same. i.e. the hub cannot traverl further than the top of the wheel for example.
For additional info, you could also measure the loaded and unladen ride height (hub to fender) to give you an idea how much your suspension compresses under load and how much travel you have in each direction (up-travel and down-travel) In an off road rig, down travel is usually the greater of the two, at least in the rock crawling world. I am sure Chris will chime in with more detail on how he sets up his vans.