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 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.