To answer your first question, the way I always understood it was this. There actually is (in the show) a conspiracy among a select group of powerful people. Not everyone is in on this conspiracy. Some of the activities of this conspiracy result in a lot of weird reports (ie, aliens).
Now, if they put a competent set of investigators on this, a good investigation should uncover the conspiracy, so they don’t want that. On the other hand, if they exert their power to keep all investigation away from these unsolved cases, their presence becomes obvious. So they do something in between.
They take “Spooky” Mulder, who has a bad reputation for believing Kooky things – so that people won’t believe him when he finds evidence of aliens or the supernatural. (It also helps that key conspiracy members think they have some personal leverage on him, because of his family history and connections.) You add a competent, but skeptical investigator (Scully), who you figure will never believe in the aliens even if they stare her in the face and abduct her. And you take every weird, unsolved and unsolvable case for the last umpteen years, mixed together with the actual cases that are connected with the conspiracies activities, and you put them all together (they do seem similar, after all). It’s pretty clear to me that they expect the team to fail, and yet the bureau has done its job investigating these cases. Ergo, the conspiracy will stay hidden.
But the team is more successful than the conspiracy wants. They didn’t count on Mulder cross referencing all of those cases and being able to see patterns and make connections that he wouldn’t be able to otherwise. They didn’t count on Scully being willing to use her skepticism to finally realize that some of these things were really true – when she sees it with her own eyes, and when there is no other explanation yet. They didn’t count on the team gaining credibility from solving some “supernormal” cases when they aren’t opposed by the conspiracy (because they aren’t related). They didn’t count on the two getting support from Director Skinner, who seems to want the cases genuinely solved, but has the good sense to tread carefully around the conspiracy until the evidence is firmly in place. And they didn’t count on a few traitors in the conspiracy helping M&S out occasionally because the conspiracy has gone too far. Or, for that matter, splinters within the conspiracy working at cross purposes, who occasionally find it useful to let M&S find out something.
As a result, they have to humor them, sometimes directly oppose them, demote them, move them off of a case, or give up sometimes. And all of this, too, generates more connections, evidence, or leads for the team to investigate.
That’s my take on it.
As for question #2: Well, it seemed to me that the questions from the first season get answered (sometimes more than once in contradictory ways, but answered), but each season generates more questions, and by the end, it isn’t wrapped up neatly. Nonetheless, there are plenty of enjoyable episodes in the meantime.