It should work out fine. Java moss will adhere to just about anything and little clumps of it may grow on the ecocomplete substrate,creating a little green carpet that fish or fry can use as cover. It gives the tank a natural if somewhat messy look.
If you want a cleaner look to the tank with no intermingling of moss and substrate you should get rid of the java moss. It can also be a hassle if you have a strong filtration system that attracts the moss to the filter uptake.