Personally, I would consider a jackshaft as an upgrade and use it if you already have it. Sometimes it is nice to be able to adjust/play with the final drive gear ratio. If you are riding off-road and/or hills (low speed) you can gear it lower so you do not overheat or burn up the clutch. On the contrary, if you riding on flat/smooth pavement (higher speed) you can gear it higher.
Michael