What do you mean? Do you add the FX on the master? Or, you don't know how to automate the low pass filter parameter? If it's the last one, you simply have to add an automation track and create an empty pattern, then you can link the parameter by ctrl-clicking on it and dragging on the empty automation pattern. The last thing, then, is to draw your automation.
Just see a video like this or search lmms automation tutorial on youtube.