The current ImageMagick (IM) version is 6.3.2-1. The last Windows installer version is
6.3.2-0 (
Cygwin has 6.3.0.1-2). Unless you mean to say the -0 release misses the scripting stuff you need
Normal Installation lists the steps to use the installer as well as advanced installation. Deinstalling is favoured, but if you can't uninstall or upgrade, you can safely install it in say another directory as long as you use the %PATH% it's in. I would not install over Cygwin, any exisitng linkage IM DLL's could break. If you plan to do it anyway make a file and registry backup beforehand.