Adam,
yes, the purge system will work on secondary filter if your purge pump is working. Loosen hex bolt on secondary assembly, exposing o-ring on bolt. Push purge button and let run until you get fuel pushing out. This allows installation of secondary filter without contaminating fuel going into fuel system. Filling secondary filter is not recommended unless your purge pump is not working. If purge pump is not working, best option is to install manual pump on secondary housing to purge air. Also, last option as Dave stated in above post, fill filter with fuel into outside ring of holes, with center hole plugged, being very careful not to introduce anything into center hole on filter. Hope this helps.