I've just finished my first season in the MLS as Chicago, winning the MLS, LA won the Supporters Shield, though. ):
I've also read plinie's guide, it's alright but some rules have changed. The main things I've found are:
Drafts suck.. Like they just suck. The players are terrible and you usually have to pick 18th [if you do well] so you get stuck with the absolutely terrible players.. Get rid of your draft picks if you can, players are better.
Trading between MLS teams is the way forward, don't waste your time trying to sign Guti for £30,000 when you can get good MLS players. You sign players by swapping draft picks, international slots, player exchange, and by spending you allocation fund.
If you want to sell a player use the "Offer to MLS clubs" option, it's awesome and you get the deals done the same day.
If you do sign a designated player, remember that £4,000 from their wage goes towards your salary cap.
The salary cap increases every year, first year I think it's around £32,000 p/w, take notice of that, it's the most important ruling!
You have a set amount of international slots, it's between 5 and 10, so sign as many Americans as you can.
GA, AA, & Dev players don't count towards the salary cap so sign as many them as you want without worry.
And, you can sign scouts.
In the league the top three qualify of each conference for the MLS cup, then 4 other clubs qualify for a wildcard play-off, to qualify for the MLS Cup.
There are 3 major trophies: Supporter's Shield [Club with most points across the two leagues], MLS Cup [Basically the Superbowl], US Open Cup [Some crappy cup that nobody cares about].
There is more I could say but I CBA and half the fun is finding out all the wonders of the MLS for yourself!