How to determine individual wing loading of a triplane for stress analysis?
A stalled wing will still produce considerable lift, so it is not on - off. That said, the best you can do is to model the lift distribution at least in a vortex lattice code which correctly computes the mutual interference. This will give you very good results for attached flow and unstalled wings. 

But triplanes have successfully been designed before the availability of computers, so for a first approximation distribute the load according to the wing incidence. Lift will be proportional to the angle of attack of each wing, calculated from the airfoil's zero-lift angle. Stagger will increase the local angle of attack of the forward wing and vice versa. How much depends on the ratio between stagger and vertical wing distance. The first solid theory of lift distribution was developed by Ludwig Prandtl and his pupil Max Munk, whose tabulations can be found in NACA Report 458 which is for biplanes but can be extended for triplanes.

If you like more recent literature: Even a publication from 2009 refers to Munk's tables, so they should still be relevant today. However, it finds a lift difference between positive and negative stagger that – according to Munk – should not exist.

Note that with struts and inter-wing bracing the whole triplane is your bending beam and will collectively carry the lift loads. Only with cantilevered wings will you need to worry about the root bending moment on individual wings. Bending between struts needs still to be carried by the single wing but will be small compared to the root bending of a cantilevered wing.