If the skeleton you import first is compatible (same hierarchy) with the skeleton used by your animation, there’s no problem to do that.
While importing the FBX containing your animation, you can set the skeleton to the one you already imported in the import windows and the FBX will be import as an animation for this skeleton.
If the skeleton used by your animation is different from the skeletal mesh you want to animate, you also can (in some case) retarget the animation for the skeleton :
https://docs.unrealengine.com/latest/INT/Engine/Animation/RetargetingDifferentSkeletons/
I read the end of your post and I see that you already read this… But there’s no MoCap specific functionality. The skeletons are compatible or not.
If your MoCap animated skeleton is the same (or retargeted) , every things should works fluently.
You can play an animation on a skeletal mesh in multiple ways but I think that you need to learn about the animation BP :
That’s how UE4 manage complex animation blending.
As far as I know, the fact that your animation was made with MoCap has no impact on the way you will use it in UE4. An animation is an animation.