In my experience it is better to self-play on a 3d board but practice puzzles online. But I think at your strength the difference doesn't matter too much, like at most 50 ELO. But "you definitely have to be used to the OTB pieces as well as chess.com ones (if you're [playing] gonna play both)"- My Chess coach, who is a NM. He also said to practice complex but clear (for engines and GMs) endgames with much stronger players (Like stockfish itself), taking your time, and then analyze your mistakes, preferrably OTB; after that save (or write down in a notebook) that "puzzle" initial FEN and also the PGN to repeat the exercise at some distance.
The power of the spaced repetition is so much you'll get even better at endgames very fast, as well as the final part of the middlegames.
What do you think?