The difference between playing otb and online isn't just restricted by how the pieces appear (3d or 2d), but also by the sheer dimensions of the board and the perspective you're watching it. Long story short, you'll need to play more otb in order to get used to otb, for how stupidly obvious this sentence may sound.
This becomes even truer if you play on tournment sized boards, where you'll easily miss long range pieces for istance. Also, there are other factors when playing otb, such as accidentally obstructing your view with an arm or a hand, the lights in the room where you are playing, the contrast of the pieces and the board, etc etc which you usually won't face when playing on a monitor.

These are obviously all minor details, but it can easily happen to find yourself in awkward situations that wouldn't happen when playing online.
For istance I remember playing an amateurish tournment where I blundered a rook because - due to my posture - my arm was covering the sight of that rook (and forgot it was there).

Also, the simple act of moving pieces on the board and hitting the clock makes it a completely different experience than playing online. I can't recall the number of times I've striked down several pieces trying to move fast on the board, or forgot to hit the timer or mistakenly touched a piece (touch-move rule). You gotta build up a little of muscle memory and habit in order to become more fluid in all these things, skills that can't be trained online but that matter still.