I am a bit lost... The guide tells in Part 2 " Industrial Age Troops In order to avoid loss of an RQ slot, negotiate southern provinces and attack the northern ones."" Is it crucial to fight? Will be tough with EMA Units...
It may be. There are 4 main paths for the Indy Story Quests: if you fight against both North and South, if you fight against the North and negotiate with the South, if you negotiate with the North and fight against the South, and if you negotiate with both North and South. (There's also a separate choice when it comes to fighting or negotiating the first province with Chief Sitting Duck.) We can get slightly different units each way, but I don't know all the details. (I'm pretty sure that we get slightly more diamonds, if we take a more negotiate-y path.)
The 2 main goals seem to be to get through the Indy map without triggering the Indy Bonus Quests, and to get through the Indy Story Quests without triggering the Indy Bonus Quests. A side goal is to get all the expansions on the Indy map. If you fight against the North and negotiate with the South, you can do this. I don't know about the other 3 paths; I think some of them won't allow you to accomplish all 3 goals.
The Indy Bonus Quests seem to be triggered by acquiring both Las Penas and Garrincton. Acquiring only one of them is safe, though. And most people prefer to acquire Garrincton, because it gives an expansion. The path that involves fighting against the North and negotiating with the South lets us do this; I don't even think it requires us to scout Las Penas at all (which is helpful in terms of Daily Quests). I think some of the other 3 paths might require scouting both provinces, or even acquiring both provinces, or maybe just acquiring Las Penas (which would be a problem if you've already acquired Garrincton). But that would only be a problem if you wanted to get PE units while in CA or Indy.
(I'm running an experiment now where I negotiated the entire Indy map, but I'm in EMA tech and LMA story quests now, so it'll be a while before I get to Indy and see what happens with the story quests.)
If you try negotiating with both sides, let us know what happens when you get to the Indy story quests?