FishHead: you're question represents good thinking, but is somewhat incomplete.
The best strategy for WHAT to use and HOW to use it greatly depends upon the targeted specie - which wasn't mentioned.
Ex: duckweed and coontail, though both are susceptible to SONAR, are two completely different treatment-concepts in ponds that have potential for transient water (flow-throughs).
If you're treating for duckweed and you draw-down the pond ahead of a SONAR treatment, you will strand a LOT of duckweed above the waterline - where it may well survive if there's adequate moisture available (potholes, mud, etc). Then, if the treated water doesn't inundate the stranded duckweed until after the SONAR-levels have dissipated, the surviving duckweed will be able to reinfest your pond.
Such a situation might justify making a separate treatment around the pond's perimeter with diquat, above the waterline, to control any stranded duckweed.
Other than that, the draw-down & 2/3-1/3 split treatment mentioned by Ponds is certainly a valid and utilized method for dealing with transient water ponds.
Also, depending upon the targeted specie(s), you might consider using SONAR Q pellets - which have an extended release-period - and thereby helps to reduce the risks associated with unexpected out-flows following a treatment.
