Oh - I guess I should answer your questions - heh:
Anyway, I just receicved my Arduino in the mail, but the documentation directs me to Arduino.org.
Yeah - my advice would be for you to get familiar with the issue, then decide which side you want to use. But let me let you know - this site (arduino.cc) and these forums have been here since at least 2009, and I think a bit earlier (2008? 2007?). All of that content, all of that expertise - it's here, and the really old stuff (back before the site changed what bulletin board software it used) has been archived (read only for that really old stuff). The "old-timers" are all here. This is -the home- of the Arduino community - love it or not, I guess.
I've read up a bit and understand there are some legal troubles.
The word "some" is a bit of an understatement - as I noted in my first post, this whole situation reeks of an extremely hostile takeover - and likely a very illegitimate one as well. Ultimately, for better or worse, the courts will decide.
My question is: Does this mean there are now two IDE's?
That I am not sure of - maybe. If you see an IDE on the arduino.org site - or if it has a Github repo - check out the version info; check out the code (if you understand it). Likely - they have changed it, branded it for themselves, and make no mention of arduino.cc or the founders.
For what it's worth - IIRC (or it may have been removed) - the "official" IDE from arduino.cc had a check in it to pop up a message saying that the board being used was "unofficial" - it wouldn't stop the compile or upload - it would just "warn" the user. I'm not sure why they did it - whether it was "dig" at the arduino.org owner(s) - or if it was something else. But they had a way of reading the Arduino (maybe the USB ident stuff?) - and spitting out the message.
I think I have the one that is on Arduino.cc as it is in the Linux mint repos.
Or are they both the same?
Likely the one in the repo is from here (arduino.cc) - as I noted, this whole thing by arduino.org is a market fragmentation and takeover attempt (IMHO) - but I don't think they have everyone on board or "fooled". But - as this thing drags on (and it will, the court system being what it is) - this confusion will continue, and it is inevitable that the arduino.org stuff will seep into other places, furthering the confusion.
It should also be noted that one of the very late models of the Arduino (I think the Due?) is wholly owned by arduino.org - not arduino.cc; I think that board was dropped (? someone correct me!) from the arduino.cc IDE - but it (of course) remains in the .org IDE (if there is a seperate one - which I think is the case?). So if you have that board (or any others made by arduino.org) - you might have to use that IDE...
Can I ask questions on these forums.?
Of course! We (try) to welcome everyone - and I personally won't hold it against a newbie who has been confused by this issue - as it isn't very clear, and took me a bit to understand it (and I still think I don't know much), and I've been around here since 2009. Just continue to study the issue from time-to-time, keep tabs on it - but don't stress over it (because there ain't anything you can do 'bout it!). Instead, focus on your project and learning the Arduino, and becoming part of this community.
Because ultimately - WE are the Arduino - even if both arduino.org and arduino.cc ceased to exist tommorow, this community (but maybe not this forum) will always be around - and something new would pop up to replace things. I am absolutely certain of it (if I have to do it myself, I will).