There isn't a set best way to get back to the stage should you be on the ledge. What's important is that you mix it up. Standing getup is a lot more viable in this game, and since a lot of people are still hardwired to play like it's Brawl, you can get away with more standing getup options than you'd think. I've been using standing getup>Bowser Bomb a lot more often, and it's just silly how much I get away with it.
Remember that Bowser can actually recover from a lot lower than most people expect, especially with his buffed recovery in this game. Save your jump NO MATTER WHAT, and try your best to stay low, unless you're playing an opponent you know is spike-heavy or can gimp you easily, ie Luigi with his cyclone. But again, mixups are key for not getting punished.
I would encourage you to play around with your options when recovering back from the ledge. You can standing getup, roll, jump, ledgehop fair, ledgehop nair, ledgehop dair, ledgehop Klaw, ledgehop Firebreath, ledgehop Bomb...you get the picture. Try using different options more often and figure out what options you like best--and what options you're going to save for trump cards.