off the notch or bridge to the axle will be the most beneficial way to mount them on an overaxle setup most likely. You want the shock to be as straight as possible. But if your ride is too stiff, maybe just switch to a standard monroe shock that has the travel you need.
http://www.monroe.com/catalog_lookup/ocl_miscappinfo.asp
use the mounting style sheet and dimension chart.
Air over axle is always going to be a stiff ride, simply because you have to ride at a higher pressure to achieve lift. Say your ride height is 80 psi compared to someone whos bags are on the bars who may be able to achieve the same lift at 40psi. I'm not sure what you have for bags now but you will get the smoothest ride out of either a sleeve style bag or a large diameter bag like an RE8.