Mike:
I have never used a unit like that, but I would think the best place for the
tuning aid would be between the tuner/swr meter, and the rig.
I suppose you could try it both ways and see if it makes a difference.
As for the Yaesu rig, I have never used one. My HF equipment is all Icom.
Hope this helps.
Best 73 from Tom Behler: KB8TYJ