If you want to obtain the best results, I’d suggest you to create a skeleton that matches the bones hierarchy of your motion capture data, so you can easily “import” or procedural generate animations.
Then, you should use that skeleton for your characters on your project. If you already have a model, then you should do the rig again.
If on the other hand you are planning to sell those animations, then you will have to do some retargeting, if you want to use the default UE4 Skeleton. You can also leave this step to the end user, or after the retargeting you should clean the animations up before selling them.
However, in the case of you own project, I’d go in avoiding retargeting, and set all your characters on your new Skeleton.