There is one main comics universe (it’s often referred to as universe #616), all of the Marvel guys are there, including both Avengers and X-Men and a whole bunch of other people.
There are other universes, each with their own sets or versions of the Marvel characters. Sometimes events happen where the universes intersect or characters cross over from one universe into another.
One of the more prominent alternate universes is the ultimate universe (designated as universe 1610). All the current Marvel series with titles beginning with “Ultimate” such as Ultimate Comics Spider-Man or The Ultimates take place in this universe.
An example of differences between universes: In the Ultimate universe, Peter Parker died some time ago and there is a new kid who has become a new Spider-man.
If you’re familiar with the Marvel series of films (Iron Man, Avengers, etc), those films take place in yet another universe called the Marvel Cinematic Universe (I’m not sure if it has a numeric designation.)
Note that there are Marvel character movies produced by studios other than Marvel/Disney; examples are Amazing Spider-man, Fantastic Four and the X-Men series of movies. These do not take place in the Marvel Cinematic Universe. That doesn’t mean these characters don’t exist in the MCU, it just means the MCU versions of those characters haven’t appeared in the movies yet.