can someone enlighten me on how each season's drafting system works?

Its the same every year with minor variances, but it looks like the league has settled on a draft lottery system. Every team who doesn't make the playoffs is entered into the lottery for the first overall pick. Top 3 worst teams get the best shot. Draft ensues. Check out wikipedia drafts if you want.

why are some top prospects drafted by a NHL team, but never appear until a few seasons after (via farm team at AHL?) Don't forget, this is the best league in the world. Some top prospects just aren't ready/able to make a team right away. Veterans can also be in the way with big contracts and the team has to wait (see Jofferey Lupul). why do some play immediately?

Turns out the scouts were right and the player is good enough to make the team and play full-time

what is considered a rookie season? if a nhl calls up a player from their AHL farm team for a few games, is that considered their rookie season already?

To be considered a rookie, a player must not have played in more than 25 NHL games in any preceding seasons, nor in six or more NHL games in each of any two preceding seasons. Any player at least 26 years of age (by September 15th of that season) is not considered a rookie.

I kind of understand 1st round picks...kinda...but what about those 100+ overall picks...where do these players head to?

Which round they get chosen in is kind of irrelevant for this question. Whoever they get picked by, the team owns them. From there, the team sends them wherever they see is best. Whether that be AHl, ECHL, back to juniors, or just scratch the player and have them in some weird limbo where they are not playing (see Frank Corrado)