You should set an parallel event that checks for a switch set at battle completion ($game_temp.in_battle == false) in a conditional branch then have it pop the message for you. It should occur as soon as the map is refreshed. You can see this being done in the Krones Forest map after defeating Leo. Also, thanks Jens for helping!
I have been messing around with this stuff for quite some time, but here are some images of this in the iso view. Please dont grip about my bad tileset, its meant to be a base and nothing more for setting up height levels and so on your map. You can use the template to start and create your own!
Now to the images...
Notice the new battle cursor?! (only available in ISO view)
Here is the template for the levels...
Here is the template for height setup.. this must be setup on the child map, but there will be more when it comes..
I am taking tilesets from FFT and manually converting them to this view(cause they are slightly different.. very close though). Its taking awhile, but in the end will be well worth it. Anyways I need to make a couple of other changes before I release this. Thanks again for the support.