GMs, do you have an advice about running "vertical" combat?

I've been GMing for a few years and while I am not perfect, I'd say I am fine. That being said, I haven't really ran a "3D" combat. The most I did in this regard is having giant bats grab one of my PCs and lifting him in the air. I want to try and make my encounters a bit more complex, so I was wondering if you guys have experience with it.

Thank you in advance.

EDIT: Since this was asked, we are using VTT.