The adverb comes from the adjective "apparent", which basically means something is "visible". So, for example, if somebody's desk is always messy at work, you could say: "He apparently doesn't mind the mess," because that's something you've ascertained with your own eyes.
However, in spoken language, "apparently" also has the meaning of "I guess so," "It would seem that," etc. For example, if you and your friend have invited a third party out for a meal but that person turns out to be 1 hour late (!), you could say something like: "Well, apparently, he's not coming."
In this case the word "apparently" refers not to something that you've physically seen but rather to something that you're pretty sure of.
Additionally, the word "apparent" also has this meaning of "clear, understandable". For example, if you wanted to say "I quit my job for obvious reasons," you could also say "I quit my job for apparent reasons." Thus is makes sense that "apparently" becomes "I guess that" in spoken language; you could also understand it as "It would seem clear that," "It's obvious that," etc.
Hopefully that helps a little, perhaps other more eloquent commenters will be able to offer you more!