Unless your front canard is at least 1, more realistically is 1.5 chord length(s) "above" or "below" your main wing you WILL be adding incidence to your main wing. Better off just putting them in the same plane or close and doing a rule of thumb for incidence. Gets back to where are you going to balance your plane. In other words what will your static margin be? Large SM = larger incidence, smaller = unstable! No canard lift = no incidence if you align the downwash angle of the airfoil at 0 lift to the main wing AoA.

I assume you are perfectly aware that your AoA v lift slopes need to lower on your canard than main wing right? Otherwise it really will not matter one damn where your NP is... If this does not make sense, ask.

PS. Have put flaps on a RC Cozy before with perfect stability and identical stall characteristics as the original configuration. A cozy is a 4 seat canard based on same design as the Burt Rutan Long EZ.