The return back to the tank? Probably a bad idea... depending on how you set it up. Either way, covering it up will effect the effectiveness of the filter.
If you cover the intake, it will prevent a lot of dirt being taken to the filter... cover the outlet/return... you change the flow around the tank, especially as the plant grows you might find that with not enough water movement, not much dirt is shifted to the filter and you might end up with certain types of algae or cyanobacteria.
Also got to consider the java fern, might not appreciate having full blast of filter return on its roots (assuming underside of wood?).
Depends if your return will be horisontal going down the back of the tank via the nozzle or if you use the spraybar from back to front of the tank...
Can also add a powerhead to the tank if you need to add more flow...
Depends on a lot really!