In my opinion, there are other more simplified tools that utilized apktool better (I use apkmultitools and vts (virtuous ten studios)) but people needs to know the basic right..
And I think, you need to put the java\bin directory in Path in windows system variables (or Java_home in win8). And it's better (I think) to put sdk directory (adb, fastboot), apktool and the smali jars files in the Path too, so that users can access from any folders/directory.
Sent from my LT26i using Tapatalk 2