There is no standard, universal way across companies.
Historically, the main Marvel Universe has been Earth 616 with alternate timelines (eg: The Days of Future Past timeline) being part of stories within the main books. As confusing as it has been, there have been points in time where a single character was the star of multiple books - where their adventures could not possibly take place concurrently. Spider-Man was the most guilty of this in the Marvel world, in my opinion. I recall him having something like 4 books of his own in the early to mid 90's.
In the past, there was a series called "What If..." where each book was a separate timeline separate from the main timeline and separate from each other. They had no bearing whatsoever on the Earth 616 continuity.
Roughly 10 years ago (maybe closer to 12), the Ultimates timeline was introduced. All of the associated books were titled "Ultimate [character/team name]" to make it easy to distinguish between the "main" continuity and this new set of reboots.
Your question regarding the non-Ultimate Wolverine and X-team books, while valid, makes the false assumption that they are NOT the same timeline. It's always been a little bit confusing as they're published at the same time and sometimes stories cross over from book-to-book, but one must often assume (or more correctly, accept) that certain stories take place before or after another.
When Jim Lee split the X-Men team into X-men and Uncanny X-Men, this was less of an issue as he did so, in part, to give more feature time to all of the characters. With such a huge roster, there was just no way to give attention to everybody's favorite character. But even then, Wolverine, for example already had his own book. It was meant to tell the stories of what he did on his time off from the X-Men, or before his affiliation with them.
Similarly, team books with prominent characters have always had this issue. Captain America, Spider-Man, Iron Man, Batman, Superman, Green Lantern - the list goes on and on. They're all members (at least part time) of groups that have their own comic series - and they all have their own personal books as well.
DC Comics, on the other hand, just relaunched their "New 52" where they simply wiped the slate clean with ALL of their books - not just a select group as with Marvel's "Ultimates". Whether readers like the new changes or not, it certainly does make it easier to keep the difference straight.
