And aside from certain things like the death of the Kents, it's not really all that hard. I mean, Morrison laid the groundwork for this and, conceptually, I think it works.
If you look at the history as a basis for Clark's personality, for example......in the Golden Age there wasn't really much compartmentalization; Clark *was* Superman *was* Clark, and the mild mannered disguise was just that; a disguise. Aside from keeping his powers a secret he hadn't really had to split his life in any deep, fundamental way until putting on the costume as a public figure with a secret identity (powers being much easier to hide than a full-blown public persona). Then as his career continues and he starts dealing with higher concept Silver Age stuff, he starts to lose touch with the grounded aspects of his life and starts to identify with the Super side of things more (which also ties into his growing knowledge of Krypton, as he uncovers more about his homeworld). Then in the Bronze Age he starts to find more of a balance and "Clark" starts to become more important to him again, but at this point there's more compartmentalization and a bigger divide in how he views his life, as both "sides" take on lives of their own that he has to juggle (ala Maggin). As we reach the modern Age and Clark's relationship with Lois and his co-workers deepen, he starts sliding towards viewing "Superman" less as "who he is" and more as a "part" of who he is (bringing us Byrne and his "Clark is who I am" thing). Then he begins to find a balance again. And that continues into today, where he's got a foot firmly set in both sides, where each is a mix of "true personality traits" and "fabrications used to enhance the role he's currently playing."
You have one Kent die, and one live. Fair compromise. And Johns provided a precedent back before New Krypton.
You can have Clark go on adventures as a kid, but not wear the costume or go public, like the Smallville tv show. That gives you the "Superboy" experience without removing the paradigm shift that is the debut of "Superman." And if Clark hangs out with the Legion you can have him wear the costume and use the "Superboy" name with them in the future. Fair compromise.
Most major villains, like Lex, have already found a balance between eras. Lex is both the super scientist of the Silver Age and the business mogul of post-Crisis. You can even start him off as a felon wanted by the authorities (like in the original stories), then have his lawyers pull him out of trouble, upon which case he returns to LexCorp and more modern versions.
Really, most elements can be fit within a single narrative if you're a little flexible, except for a few specific things like the Kents where you'd have to compromise or pick one era over another.