I've only done habitat manipulation around ditches to improve desirable native species but not planting of plots. However, planting near a ditch should be no different than anywhere else - except that you are in wetter ground and you likely need to be more concerned about erosion. My advice would be to plant water loving shrubs like red osier dogwood at the edges of the ditches to prevent erosion and do the plotting a few feet away from the ditches.
PS: Sometimes what you kill is more important than what you plant.