That link above is a great resource, and I wish I had had it when starting my first MLS save this year with Columbus Crew. However, I managed to scrape by in my first year, barely keeping my job and finishing 18th, to come back and win the Cup the next year.
The first addition to that guide would be that there is another draft called the Supplemental Draft that occurs in late January. Effectively, it is a continuation of the SuperDraft and you can find some really good youth talent. The second would be a note on how player transfers work.
In most other leagues, the club has X amount of money to offer to clubs to buy a player. In the MLS, transfers within the league are handled through trades. For example, say I want Clint Dempsey from Seattle Sounders for my Columbus team. I may offer to trade some combination of my player(s), international spots, allocation funds, and/or draft position(s) for Dempsey. If Seattle accepts my offer, Dempsey's contract with them transfers as well, and I don't have to re-negotiate that. Now, if I want to sign Jack Cork from Southampton, I would only be able to offer them money out of my Allocation funds (which in this case, would be no where near what Cork is currently worth). In addition to that, when negotiating contracts for my players, coaches, and non-MLS players coming in, agent fees and compensation due to other clubs comes out of the Allocated funds.
To be honest, I've found the hardest thing to be figuring out what a proper valuation for a trade with another MLS team is.
As with anything in FM, the best thing to do is to start a save in the MLS and fail for a while until it clicks. However, I hope this helped somewhat. Good luck!