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I use the yn622(c) for the canon system, and have no experience with the nikon system. so I can't really comment on how it'll work with your body/speedlights. but here's a long winded reply just for the fun of it. (:
>>>would the in-camera flash compensation level adjust the output of the wireless units with the Yongnuos?<<<
I think that in general, the speedlight needs to have what-ever function already built in, so a non-ettl speedlight will never behave as if it was ettl capable.....and any basic speedlight that you could not set the levels of from an in-camera body menu won't get that ability just because it's mounted to a 622.
I think there are some differences in how nikon vs canon systems deal with fec, so I'm really not sure how to answer your question. what I can say is that in most cases (with fully capable body/speedights) the yn622s seem invisible to me. any flash related setting I have the option of from the camera body menu will work. fec, high speed sync, ett-l, second curtain and so on. I'm not sure how your system will behave if your setting power levels from the camera body menu (not ett-l) and then dial in FEC.
>>>What about if there was my SB900 on top of a yn-622n on my camera's hotshoe...would it be impacted?<<<
the speedlight mounted to the yn622 (on the body, or more accurately the one in transmit mode*) will always be in group A.
(the fallowing is just babble)
I have a mix of camera bodies with different levels of on-body flash control.
but I've found there are a few work-around bits you can take advantage of:
you can have the 622 run in "mix-mode" so that the speedlight mounted to the 622-on-body can run in ettl, while other speedlight groups are manually set. but I have no idea how nikons system will handle this.
(*)one cute thing I've found about the yn622 is that it'll always use the last settings it was told to use unless you've told it to do something different-
that is to say that from my canon 1d3 body (with full on body flash level setting menu) I can set the power for each group or even just use ettl (on some speedlights you can dial in fec for that unique speedlight from its own menu) and after a shot I can remove the 622 transmitter from the body, mount it to a basic radio trigger receiver (yn rf-602 in my case, or any camera body with a dead simple hot shoe) and then trigger the the 622 from the 602 and the 622 will keep repeating what ever the camera body menu settings was. this is very handy if I want to trigger the 622s from a different body (any brand!) even if that body doesn't have any of the functions built in. such as a very old canon, a fuji, or even some old nikon film body I don't even know the name of. I can take a shot from the canon body with manual body exposure settings in ettl, then use some prehistoric body with the same exposure settings and the speedlights will retain whatever ettl settings the first camera body set.
the pc port on the 622 will have trigger-only ability, any level settings or ettl must go into the hot shoe foot on the transmit unit, or be mounted to the hot shoe on any receive unit (622 magically determines if they're 'spose to transmit or receive, and they get it right). but the last-setting rule from above still applies for 622 shoe mounted speedlights.
the focus assist light from the 622 is very nice. projects a grid rather than a bright illumination lamp.
hope some of this will answer your questions. I really like the radio popper system and use it for studio strobes, but I personally find the 622s far better for any speedlight control, and they cost less as well. the radio poppers use some odd-ball battery that I've never found a good rechargeable set up for that I'm really happy with, while the 622s use plain old AA batteries.
someone put together a comprehensive user handbook to replace the laughable one supplied by yongnuo. it's for the canon variant, but give it a look...