If I were you I would use only one power source for all my SYSTM workouts. That way you don’t have to worry about differences in accuracy between the pedals and the trainer and will always have consistent power numbers when training indoors whether in ERG or Level mode.
So, while you could use the cranks as your power source and the Direto in level mode, you probably want to avoid this for the reasons I said above.
To find which level works best for you at different types of efforts you can use any Open Vid eg. 30 mins, and test out what a sustained FTP effort feels like at level 1,2,3 etc and which gearing & cadence helps you maintain that effort. Then, do the same thing for MAP and AC efforts to see how different levels feel and what gearing combo works best for you (and the best one may be different between different types of efforts). Same thing again for Sprint efforts, see what level works best, what is the best gear to start in, whether you need to shift gears and when.
FWIW, I found that level 2 pretty much works for everything for me and for the Sprints I usually use my Big Ring and toward the smaller end of the cassette.
Hope this helps