Not all villains will need to worry about this. Starting villains should focus on getting established - several solid capers, a known name, integration into the larger super community. Veteran villains have already firmly fixed their own narrative in the minds of the public. It's the mid-level villain - the one who can make the front page reliably, but can't control what they print yet - that has the most to worry about.
Let's start with the fundamentals of media management. Media is a plural (the singular is "medium"), and refers to tools used to store and forward information. Most of the time when people say "media" or "the media", they mean journalism, aka news media. This includes newspapers, magazines, journals, TV, radio, and the Web. "Media management" is the ability for the villain to influence what other people say about him or her via any of these channels, and/or to have influence when speaking directly through them.
I talked more about building relationships with the media earlier, so for many centralized forms of media (TV, radio, print), you should refer to that guide for how to proceed. Much of the media today is built around the concept of "access" - a journalist's ability to get privileged information from a special source - and if you are big enough, you can try and bargain access in exchange for reporting things you want reported. It's a delicate balancing act and takes time and practice to get good at doing, so I suggest working your local channels first. Only move to the national media outlets once you feel confident in your technique.
That leaves managing the "new media", of which "social media" is a subset. This is basically the Web - YouTube, Facebook, Twitter, and probably a bunch of others I either have forgotten about or never heard of. There's two ways to proceed here: get the ear of influential new media personalities, and manage your own social media presence.
Like traditional reporters, "access" still matters to bloggers and vloggers and whateveroggers tomorrow holds in store. Thanks to a perceived rivalry with old media, one thing many bloggers prize is better and faster access to a source than the "dinosaurs" in print and television can muster. They're the guys with the camera at the crime scene, metaphorically speaking. This is the theory behind websites like Brickwatch, which collect and collate information about super-battles in near-realtime.
If you are interested in building relations with such people, you'll want to pick a few personalities to interact with, then read their sites. Get a sense of what interests them - every blogger started with an itch they wanted to scratch, and many are idiosyncratic in what they'll cover. Find out what you want to say that works with their angle, then get in touch with them.
Alternately, you can go directly to Twitter, YouTube, and so forth. It's not as easy as getting your own account and just posting your crimes, though. There's several reasons why you should work with an intermediary or assistant.
- Terms of service. All modern electronic services have rules about what content they'll let people post. For example, YouTube's section 6E ("Your Content and Conduct") forbids content that's "contrary to applicable local, national, and international laws and regulations". In general, villains posting their own stuff get flagged and banned. However, the government has pushed back against this several times, by requesting that such services retain the content. Their argument is that useful intelligence about villains' activities can be gleaned from what they post. Of course they're notoriously vague about how, when, or if this really happens, but hey, it opens the door to doing so.
- Security. If you ask Comcast to run DSL to your lair and then post from there, expect the Feds to come knocking. By having someone else post your content, or by doing so from innocuous locations (Starbucks free wifi, for example), you avoid being traced back. Learning all the rules of securely posting content comes at the cost of your other villainous skills, though - it's usually better to leave this sort of thing to someone who knows what they're doing and is sympathetic to your cause (or who stays bought).
- Domain expertise. I don't know a thing about search engine optimization, aside from what it is. I have no idea what cross-posting tools are the best, or which support Google Plus vs. Tumblr. And I don't know these things because I'm too busy being a kick-ass villain. Leave the specialty tasks to specialists.
Many villains work with someone (or pose as someone) who claims to be "documenting <villain name>'s nefarious activities for the authorities". This excuse is paper-thin but it's enough to keep videos from being auto-flagged. In general it will not hold up in court (and yes this has been tested).
Finding a new-media biographer isn't easy. This is generally the sort of task you can put onto a villainous apprentice, if you have one - and provided she isn't grounded. Never let such people into your lair, or give them details about your plans ahead of time - after all, they might be planted. But should an opportunity arise, feel free to take advantage of it, if you can do so cautiously.
So what do you do with all this? In short, you protect your good name. If you see crimes attributed to you that aren't yours, sad to say but you need to tell people that. Accused of murdering innocent children, and it wasn't you? Set the record straight. Reporter said you "bumbled through the crime"? If you didn't, tell them why they saw what they saw - or demand that they get a more reliable source. Like I've said before, the most convincing explanations are those with plausible details, and you can get into (safe to reveal) specifics of your crimes in ways nobody else can. Use this inside information to prove your identity, then use that credibility you acquire to say what you need to say.