The answer to this is... yes or maybe or no
Yes) You can use a mod such as
http://www.minecraftforum.net/topic...ilters-scripts-a-new-map-making-tool-updated/ (in game MCEdit) and it will be able to use filters/import schematics ect without "many" bugs. for example MCEdit doesn't like microparts much so it may not import those.
Maybe) If the chunks you are editing are currently "unloaded" and you save in MCEdit when a player goes to that area and loads it, it
MIGHT work. (if it does good..if it doesnt save properly for example if a player loads the chunk half way trough saving it could corrupt the chunk completely and reset the chunk)
no) editing the map from an external program such as MCEdit is bad and can cause world corruptions, crashes, explosions and world war 3.