Easiest way is to just extract everything in the toolkit into one folder, seperate from anything else (so not the same folder as you're using to make your game).
Then, you'll want to:
Data folder
Put all your data files in here. By default, the Data folder already contains copies of every graphic set; you can delete ones you aren't using if you want. If you're using any that aren't in there (custom ones, converted Cheapo ones, etc), make sure to add them. Pretty much, every file for your pack that isn't a music file should be in here.
Music folder
Clear out everything that's already in here (unless you're using them - if you don't have your own, you might want to leave frenzy.it and gimmick.it in here). Put all your music files in here.
After doing that, does it work? If not, can you give more details on exactly what happens (see my last post).