It's more like you have a mission with one area and a boss then you complete another mission in a different area with a different boss. When you merge the 2 missions you get enemies from both missions, the area will be either from the first mission or the second and you will also get one of the bosses.

On top of this some of the missions you create can have hidden properties (like a certain rare enemy appears or something).

The rewards work by making certain missions (a specific area with the specified enemies and boss). Once you complete the mission you get a "treasure" which can be used with other "treasures" to trade for uber items to upgrade your weapons etc. It's kinda hard to do in Japanese so I have yet to finish any of these on infinity. I can imagine this working pretty much the same in PSO2.