[ntsqd]

Presumably you've chosen shocks with enough travel that they are not going to limit your travel. Hitting the limit of the shock's travel before the rest of the system limits out is usually a bad thing. The worst case is at full compression. Rarely does full extension happen at high velocity, but full compression nearly always happens at high velocity.
High velocity full extension is pretty hard to do since you only have spring rate and axle mass working for it. Usually those speeds are low enough that the shock can handle it without damage.
High velocity full compression is much easier to do since you have vehicle speed and mass working for it. Rarely are those speeds slow enough that the shock can handle it without damage.

So setting up the mounts to keep the shock from full compression when the suspension is fully compressed is my first priority. This would be easy if the bump-stops were part of the shock and I didn't need to worry about articulation. The further away that the bumps are from the shock, the more that articulation affects where the upper mount needs to be to keep the shock from becoming the new 'bump-stop'.

I don't really cycle the suspension for the lower mount. I do take the cycling into account when deciding where to put the lower mount since that drives where the upper will likely be. I find it simpler to fix the lower in place and then go to fully articulated compression to find the upper location, rather than trying to worry about where things will also be at full extension. If the length of the shock is right then full extension is not important.

If this were some sort of off road racer I would first remove the bump-stops and then set up the upper mount based on metal to metal contact. The reason is that off road racing is hard on bump-stops and you can not count on them always being there. Once they're blasted off the vehicle I still want the shock to come home in one piece.