Well, first off, I always animate the body first. Most animators get the body stuff blocked in, and then do a rough pass of limited facial and eye animation before really diving into the facial performance, so it's a very common and normal challenge to be doing the face as a secondary pass.
The main thing to consider here is timing, and planning your facial expressions to hit at moments that complement the body performance rather than distract from it.
For example, if it's important to your story that the character is sneakily stealing a pen from a desk, then it would be a really bad idea to have his eyes doing huge radical movements just as he steals the pen and puts it into his pocket. If the eyes are really going crazy, everyone is going to be looking at his face and totally miss the story point about the pen being stolen.
Beyond just basic complimentary timing, you also want to time the emotional beats of the face to work well with the body. I tend to try to let the face lead the body by a frame or two (or more, in a slow realization or protracted emotional change) with the idea that the face and eyes will betray emotions quicker and more immediately than the body language might.
An example of this might be a scene where the character is realizing that the love of his life doesn't actually love him in return. You've already created the body performance of him eagerly offering her a flower, and then the shoulders drooping as he hears her rejecting, letting his hand fall to his side, dropping the flower, hanging his head, etc. The most important facial stuff in this scene will probably be his eyes searching her eyes for the truth as he hears this devastating news, and then the whatever you choose to have his face do as the news really sinks in.
Does he stare at her, disbelieving? Does he start to cry? Do his eyes defocus and he just stares into the distance? Whatever you choose, you should consider letting that facial performance happen before his shoulders drop, before he drops his flower, etc.
The body performance SHOULD be telling the story in itself, so be sure to spend enough time making sure your body mechanics work and the emotions read in your poses. The face should be kind of the "cherry on top" that really seals the deal, it can't carry the whole performance itself or the character will just feel stiff and lifeless.
Good luck and have fun!