The good news is that your readers will likely keep up just fine, because we all have many names. Off the top of my head I can think of six different names I answer to, contextually; what my wife calls me, my kids, my mom, my friends, colleagues, or the cashier at the grocery. Names are contextual.
I too am writing a character who goes by numerous names, so much so that the character isn't even given a name at all until the second chapter, nor does the reader ever learn his birth name. And it works, because a priori, he only thinks of himself in first person, so even when narrating in his voice, his name doesn't matter. It helps that I'm writing limited third-person unreliable, but even if you're writing omniscient, you can use names as a story-telling device, not just a facet of the story.
For example, if I open a chapter with:
"Dammit Dad, where's the key for the f#$@ing Subaru!"
Think of how much information this conveys. You can assume the speaker is probably old enough to drive, that their home life is probably not rainbows and roses, or perhaps unorthodox, and we have established tension. Not bad for not even using a proper name...
Now let's say Dad's best friend calls him Bart, and his wife calls him Barry. Once you establish their respective context, the names themselves will provide that context to the reader, and not rely on it.
Bart gulped the rest of his beer and slammed the bottle down. "Welp, I'm out."
"Out?" Mark scoffed. "What, don't wanna be late for dinner, Barry?"
"Which one of us is still married, smartass?" He slapped a twenty down, then floated another to Mark. "There's for your dinner. Later."
See? Mark's use of "Barry" here gives reader context: sarcasm.
Aliases are really no different than any other name, they just might take a bit more contextualizing to establish attribution. You may only need a single sentence for "Dad", whereas it might take an entire chapter to establish a different persona. Or maybe not.
"Well look what the cat dragged in."
He glanced up from his phone and did a double take. "Holy sh-- Angela?"
"Haven't heard that in awhile," he grinned.
But if you're uncertain whether something is working or not, and you can't get beta readers to provide feedback, another thing you might try is to read your story out loud. A partner is handy here, but even just to yourself can often suffice to underscore clunkiness or confusion. Not a single sentence, mind you, but a page or so, to give you a feel for flow and cadence.
If that still doesn't provide the clarity you need, you're not sure if you need to change it or not, then go with your writer's instinct; if it's telling you something is off then yeah it probably is. Try again, or if you're truly stymied, bookmark it and come back to it later. You might stumble on a better way of doing it a few chapters down the road. But don't let it break your writing flow, and don't overthink it.
Sometimes you just gotta trust your reader. Tell them a good story, and they'll work out the minutiae, no matter.