@jamie75 is correct that you shouldn't be in game when the maps are installed. The game loads the map file while you are in game and won't overwrite your existing zone, or load the existing zone while you are in the zone. You should camp out to character select screen at a minimum (on all characters if you are boxing) and then install the maps. Ensure that layer 1 is visible as that is the default layer for maps, with layer 2 being the MQ2 layer (which shows your spawns location/names/radius' etc) In some zones, like POK it will be drawn on the base layer.
I've never personally used an alternate map setup (IE: I've never used a sub-folder)
It's also possible that maps as a sub-folder may not read spaces in the file names. This is typical behavior for things such as macro's where it can't have a multi-word file name and you may possibly need to remove any spaces in the name of the file and exchange them for underscores _ or remove the space all together and just have it as one word.