You should be running the jasshelper with the command line (steps 2 and 3). Step 1 can be done with the windows explorer though.
In step 3 when you run jasshelper, you can specify the arguments:
"jasshelper.exe" --debug common.j Blizzard.j "%path_to_output%\vf.w3x"
I will try to explain in more detail.
You have one map you are actively developing. When you want to test, play or release the map you have to use jasshelper so all the scripts work.
In order not to break your original map, you first copy your map to different location and only use jasshelper on the copy.
1. navigate in windows explorer to your map
2. copy the map to a different location
3. copy the path of the copied map (map path) to a text file, so you can later use it again
4. navigate in windows explorer to jasshelper
5. copy the path of jasshelper (jasshelper path) to a text file, so you can later use it again
6. Start the command line: Hit the windows buttons and then R. Type cmd and hit enter. This will bring up the command line.
7. Copy the jasshelper path from the text file
8. Enter cd <jasshelper path> in the command line, where<jasshelper path> is the copied jasshelper path
9. Copy the map path from the text file
10. Enter "jasshelper.exe" --debug common.j Blizzard.j <map path>, where <map path> is the copied map path
Now jasshelper should do its magic and the map at map path should run.