It is possible to break up one map into a number of different areas as needed. Since it is possible to set groups of enemies for the player to encounter in a particular area, you can use areas to fine-tune the locations where certain enemies appear.
To create an area, right-click on a map in map tree view and select [New Area]. The area will be created for the selected map. You can select the range that the area will cover by clicking on [Area Position] in the window that will appear. Drag within the displayed map to set the rectangular shape of the area.
Now all you have to do is set an enemy group for [Encounters] and that enemy group will only appear in the area you have selected. The encounter rate depends on the settings for the map on which the area was created.