The best way to know exactly what it does is to try it.

If you have all the tracking features checked in the Animation menu, you probably will not need to do any alignment. Both position and rotation are properly tracked now. That means when you add a motion it will be in the correct location and facing the direction the character was already facing.

If you remove the first part of a motion, then you will need to us the align tools.

To keep it simple:

Align/body part moves your character so that body part is aligned with where it was in the last frame of the previous clip to play the next clip. That is the location in the Preview window of the character.

Align Whole Clip sets every single frame of the new clip to the last frame location of the previous clip.

I finally understand it. I'm going to explain it in my own "dumb" way for anyone else whose head this might've gone over. I appreciate everyone who pitched in, they already explained it, but here's the dumb language that I understand it in:

Align Whole Clip (and then choosing a body part like "left leg"), means the entire animation clip will revolve around that left leg. That foot is planted, and will NEVER move off the ground for the duration of that clip. That's the bottom line. That means any animation clip that involves the foot moving (lifting off the ground), would not be suitable for this, like walking. The walking animation will not work properly, since that foot will never move, and so the character will just weirdly approximate a walking movement, without actually moving forward or moving his leg off the ground. Other types of animation it wouldn't work for is like a backflip, etc. Anything where your character is supposed to move that body part you selected.

Align (and choosing a body part, right leg), is pretty much what everyone has been saying, and I don't really have "dumber" language to say it in. Wherever the right foot (it's FOOT, not really leg, to be accurate) was in the last animation clip before this one, is where this clip will start. You're aligning that body part, just as the name implies. The character will still MOVE forward or backward (and any other direction in space). So this would be ideal for walking animations (specifically, to FIX them). 

I just needed to understand the concept of a foot being "planted" and never moving from that spot (i.e. Align Whole Clip), versus a very unrelated feature (in my opinion) of simply Align, which obviously does what I explained. Also the fact that Align Whole Clip has the options to then choose a body part totally threw off my understanding. Something about the name makes it feel like you're aligning the "whole" thing, only to see, that you're STILL choosing a bodypart anyway. And that sent me down the rabbit hole of confusion, trying to differentiate, "ok, the Align function let's me choose a bodypart, fair enough, that makes total sense. You choose align, and then you click the bodypart you want to align. Wait a minute, Align Whole Clip also let's me choose a bodypart to align? How are these things different, and what am I aligning?"

I believe the explanation in the manual for "Align Whole Clip" could include language where it basically outright states, "that body part will be PLANTED for the rest of that animation clip." The explanation as well as the sample animation in the manual definitely explains it, and says thing like "the rest of the animation will align to that bodypart," but it's not actually obvious what that means unless you already have a fairly good understanding of the terminology. I would've liked to have straight up been told, "hey, dummy. whatever bodypart you pick, that part's NEVER going to move from its current location."

I don't know, maybe it's obvious to everyone but me. In my opinion, the term "Align Whole Clip" should be renamed. Not because the term is not accurate, but because of it's similarity in name to the completely unrelated, yet adjacent function of Align. You do both of these functions for totally different reasons. You do one to plant a guy's foot to where he doesn't move that bodypart, you do the other because you want to align his foot (or arm, whatever) to the previous clip. To me, totally unrelated, other than the fact that they both involve the manipulation of a motion clip.


I went into granular details with my explanation, and giving my anecdotal thought processes for anyone who may have been as confused as me, and had similar thinking; maybe seeing these same thoughts they may have, will resonate with them.



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Cliff's Notes:

Align = match the selected body part to the position it was in, in the previous motion clip, so they can match, or be aligned.

Align Whole Clip = surprisingly, nothing at all to do with the above, similarly named function. This is for when you want to LOCK DOWN a body part in space. Rest of the avatar's body part's will move, but not the body part you chose to "align." Because you're not aligning anything. You're LOCKING it down.

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My iClone short films: https://www.youtube.com/iClone316