1. There needs to be at least a year’s worth of forewarning for creators and planning before they even begin taking steps towards it actually happening.
2. Put out a few core titles of the reboot BEFORE relaunching the whole line. For instance, Superman #1, Batman #1, etc. as Ultimate-style “GET IN ON THE GROUND FLOOR…OF A WHOLE NEW REALITY!” books to lay down a foundation of who these people are and what their world looks like before bringing the whole line along with them. That way you don’t have to do the whole thing at once, or just put out a handful of books in one month and slowly build it up over time, and the handful of books out before the whole reboot will be huge as windows into what the company is going to look like in a year (it could even be a way in that regard to test the waters and make course-corrections prior to the full launch).
3. There need to be a couple creative powerhouse headmen. Marvel had its architects, DC had the guys writing 52? They should be the ones making the decisions about the biggest characters alongside the writers of the individual books as a means of quality control.
4. Put out a Secret Origins-type book immediately.
5. Probably there’s no need to wipe out the old continuity in-universe? There’s an infinite Multiverse at both of the Big Two know, you could just move to looking at one of the other Earths, with the old reality out there to look back at anytime you want to. You miss out on cosmic shenanigans, but you could still have one final great battle as a closer to that world without actually destroying it, and lots of fans would probably have an easier time accepting the new world knowing their faves weren’t actively being destroyed/altered/otherwise disposed of.