I downloaded the sc4 maper but when I go to use it on a map it really messes it up or doesn't work ar all am I missing something? as to were it goes?
There are a number of threads about this in the SC4Mapper (http://sc4devotion.com/forums/index.php?board=128.0) forum.
Have a read through there as I am sure you will find an answer to your problem.