Of course - only the one in TTl would give out the pre-flash.  Hence "getting to 'M' "  ....  
Recommended option would be to go manual using the on board commander  mode to trigger the one and then make adjustments based on output  desired (best done with light meter or failing that trial and errors)   If I could get both to work on CLS then I could control the output of  that group from the camera (have to play with how they fit into that  softbox to get both of the CLS sensors out of the box and only the  lighthead in the box.
		
		
	 
Yeah, there are many TTL complications. 

    The Commander is simply incompatible with other systems, including  real actual manual flash mode (the mode M on the flash menu). The  handheld light meter is also incompatible manual gear, designed for real  actual manual flash.  Because, the Commander, even if in its MAN manual  flash mode, still outputs many flashed commands, like to transfer the  power level from the commander menu to the remote flash(es).  All that  flashing will trigger the optical slaves early, before the shutter  opens. Then the meter will meter what it sees (that weak early command  flashing).  And this flashing is far too complex for the simple S2 slave  options to deal with.
There are several reasons (detailed at 
Using the Nikon CLS Remote Wireless Flash System - Part 2  ) why the Commander just ain't gonna work mixed with other systems,  including mixing with real actual manual systems.    The handheld meter  failing with the Commander MAN menu might be worked around by IR  filtering the commander, and the meter not being too close to the  Commander. But "compatible" is a word far too big.  
 
The best advice is if using the Commander, then use it, for all flashes.   Otherwise, use another system. The Commander is much more direct line  of sight though, often works well, but problems can become much worse  than with the simple optical slaves. The remotes do need to see the  commander.
	
	
		
		
			I have to remember that the TTL pre-flash metering by the commander unit  is done by 'group' (e.g. A, B, or potentially C if available via an  mounted flash or Nikon CLS Commander unit) You are recommending one  flash per group, hence two or maybe three flashes.  I tend to think of a  'group' of flashes as more than one but I understand what you are  saying. I've been using three flashes under Nikon's CLS, four if you  count the pop-up as controller.  So again, if I want to control more  than a couple of flashes in TTL that is another reason to get radio  control system (and even then it may be hit and miss.
		
		
	 
Yes, one group can control more than one flash simultaneously.  But yes,  I do tend to imply a group is one flash, since all shared have to share  the same power level, which is NOT individual control.  If you want to  control individual flashes, that is one flash per group.
My notion is that commander seems great (and quick and easy) for two flashes in umbrellas, but more becomes a big deal.
Multiple manual flashes and a handheld incident meter becomes the norm  for more flashes, and for more careful critical setups. Much more  control and versatility is possible then.
	
	
		
		
			RE: Ratio etc
Been wrapping my head around the ratio and balance with lighting.   Ambient vs flash lighting and the positioning of the lights.  Lots to  learn here.  Learning how adjusting shutter and adjusting aperture works  differently with the lights on.  The duration of the flash is another  factor, through in HSS into the mix and it gets even more complicated.   Reading how P.Wizard does HSS differently than others was one of the  attractions of P-Wiz but probably not going that way,  ... yet.
		
		
	 
Lighting:  Speaking of portraits, the simple baseline first idea is this:
Main flash, high and wide of subject, like perhaps 45 degrees both high  and wide of subjects nose.   This mimics sunshine angles, it makes  intentional shadows for the lens to see, showing shape and curves, etc.   Adds interest, not a flat light.  (flat does have uses sometimes). We  might try to categorize different shadow patterns, but high and wide is  the common starting point.
Fill flash: to fill the above harsh dark shadows, to instead become very  mild gradual tonal changes, still adding interest by showing shapes and  curves. This gradual tonal fill is all important, to be "natural".  Ratio is the whole idea.  
The  Fill flash should be located very near camera lens axis, to fill  the same shadows that the lens sees, without adding a second set of  shadows to distract.  This means the fill flash has to be back near the  camera, so the lens can see around its umbrella.  Behind and above  camera is a popular place for it.   Fill flash level generally should be  around -1 EV from the main light, which is a good ballpark degree of  fill ratio (grayscale can use more ratio, but more ratio often distracts  from color).  Maybe SOMETIMES less ratio for ladies and children, and more for  grizzled old men, the prospector type.    So even if the fill is -1 EV,  this greater distance might mean that fill is the larger flash power  needed.
If you do that much, the result will be pretty good.  Then a background  light and a hair light can add more control of the result.
 The PowerWizard Hypersync feature is not HSS.  Similar, it does allow a  faster shutter, but it is not a constant power level for the total  duration (like HSS is).  The flash unit has to do HSS, a radio trigger  cannot create it.