I am not sure I understand correctly what you want to simulate but, the management you have created will simulate all the plants growing in the same area at the same time and, I think, it is not what you want to simulate. My guess is that you want to simulate different managements and, as a consequence, you will have to create three different management files and assign one of them to each subarea with a different landuse. Please, provide me more information about this so I can give you more information.
Regarding the kill operation, it is required to tell the model to terminate the simulation of a specific crop. To give you an example, if a kill operation is not used after a harvest operation for corn, the model will continue to simulate plant growth even after a plowing operation. In the case of a perennial or a tree, it should be possible to skip the kill operation unless the lenght of your simulation is longher than the tree life cycle.
About the proportion of your area, you can do so during the watershed designation phase. In this process, the user can define the size of each subarea (in your case each subarea can be a part of the landscape with a specific landuse) and hydrologically connect them. Please, take a lok at the APEX user manual for more information on the watershed and subarea delineation.