The solution, implemented in a patchwork fashion over the last decade, includes admonitions to use your military email account for official business only, and to use the same "chain of command" protocols for email that you use for face-to-face contact. Some units have rules for what to put in the Subject Line of emails, to make it easier for everyone to spot important messages.
But problems remain, the biggest one being a superior officer who inflicts bad email habits on his subordinates. Basically, it's up to every commander to keep an eye on bad email habits among his subordinate commanders. Thus with the spiffy new tool, comes yet another problem area commanders have to keep an eye on.
Finally, there is the system wide problem with getting a new email address every time you change assignments. While this is great for keeping the spam down, it makes it tough to stay in touch. Troops have been agitating for permanent email addresses for years, but with little success. So, in the meantime, many have gotten a second, non-military, email address. This second email also allows the troops to avoid accidentally doing some forbidden email thing within their chain of command. It's also become widely known that the Department of Defense automatically scans all .mil email addresses for signs of trouble (treason, spilling secrets, who knows what else.)
Email has been a remarkably effective new tool for the military. We tend to forget that the military is basically a large bureaucracy most of the time, and bureaucracies live via the constant stream of written information passing up and down (and across) the chain of command. All officers, and many NCOs, have a desk somewhere, a desk that they use a lot. Even combat units must deal with masses of paperwork. Email, and word processing in general, has allowed the military to get rid of a lot of the paper, and move information around a lot more quickly and efficiently . But, as always, there is a dark side. Troops and officers, over the last decade, have been entering the military quite familiar with email, and have some rather non-military ideas about how email should work. Most of these new troops proceed to try out all their bad email habits on their fellow military users. Bad idea. CCing lots of people with many messages (a few useful, but most not and many of the jokes you pass along are not appreciated.) The solution has been to establish standards. Some of them are common sense. Everyone in the military knows how the chain of command works (ie, if you are an infantry lieutenant, you cannot just walk up to your battalion, or brigade, or division commander and ask a question, you have to go to your company commander first, and your company commander may prefer that you speak to the company executive officer first.) But many junior ranking folks see nothing wrong with CCing lots of people way up the food chain from them. Big mistake. Commanders have problems with email as well, with many trying to "lead via email." Somehow, inspiring email does not have quite the same impact as showing up in person.