1. A computer-implemented method for marking-up an executable model in an executable modeling environment, comprising: displaying the executable model to a user, wherein the executable model contains at least one executable element; associating an electronic overlay with the executable model, the electronic overlay operating with the executable model without changing the executable model; receiving an electronic markup in the electronic overlay, wherein the electronic markup affects the functionality of the at least one executable element contained in the executable model when the electronic markup is executed with the executable model; displaying the electronic markup in the electronic overlay; and executing, using a processing device, the executable model with the electronic overlay, wherein the electronic markup in the electronic overlay affects the functionality of the at least one executable element contained in the executable model during execution of the executable model.