I created the parts in solidworks and the runners in solidworks plastics. When trying to make an assembly the runners go back to their original sketch. Is there any way to make the runners a solid body, combine them with the parts, and subtract them from a third part (extruded boss) to create the family tool?
I will do my best to answer the flow you are trying. The runners made in plastics are not solids that is why they disappear. Since you have the sketch from making them in plastics you can use them to make solids with runner and gates on the part level. When you have the parts with the runners and gates you can then put them in the mold assy then use the cavity function on a part level.
I go about doing this in a different way. I have my assembly with runners, gates and cavities in them. Insert a part called "as molded" and use the cavity feature to get an impression of whatever I am molding. I then open up this part and run it thru plastics. This gives me a fairly close analysis of what the tool is going to do. I can change the runner or gates in the assembly and it will update the "as molded" part. Then just mesh it again and rerun the analysis. This is just one workflow, not the only one.