Where do you put it?
Well.
Depends of what you want to do...
If you want to work only in one map, you put the script on Doom Builder's ACS editor, it'll automatically input the code for your map, and your map ONLY.
Now, if you want to do a gamemode or something similar, create a file on a pk3 or wad and put it there, then make a LOADACS lump and include your ACS lump there.
Make sure of two things:
The script number should be unique, or it will replace other scripts that may be in use; (from 1 to 10 is usually safe for maps. More than that is usually unnecessary. Check the GLOBAL acs lump to see what numbers of ACS Mike's using for 8BDM, or you'll end up bugging the game) likewise, the method of activating the script is something you need to pay attention.
For more information on script activating, refer to:
http://zdoom.org/wiki/Script_types