Depending on what micron the second filter is. The main filter will be around 8 micron, brand depending. So if your new filter has finer filtration ability, i.e 8 micron or less, it will need to be after the main filter, to catch what the main filter is unable too, if its like a 15 or 30 micron, before the main filter, to catch the larger particles to assist the main, finer, filter.