You create spawns by placing entry point. These have a number that you can modify. You should place 5 entry points. Two for the teamspawns (0 and 32) three for the Master of the Field flags spawns (67, 68 and 69), so they don't spawn in impossible positions. The game randomly picks one of these three.
You edit the number by selecting the entry point and editing the top bar that says 0. For me that didnt update it immediately so if they are still called 0,1,2,3 don't worry.
Don't think I can help you with the other question. If I exited edit mode and saved my changes and then left the game and then started a new game with my map all my changes were still there.