Yes, if you have 8 units on the map and the bad guys only have one, then it probably will be a lame fight, best to auto-resolve it. It depends on the match up, though.
The units you build on the RTS local map are not carried over, they're gone at the end of the fight, however, the better your efficiency at keeping your troops alive, the more of your troops from the big map will survive.
Another non-obvious thing Larian should probably explain better is that a War factory can only produce a number of units equal to the gold income of that country. Why? I don't know? It doesn't matter how much gold the units actually cost. So place your factories on the 2 and 4 countries on the strategy map.
