WHDLoad is incredibly easy to use... dont know why the problems.
First you need the ROM images, either from Cloanto, made yourself, or from warez sites on the net. Install these in DEVS:Kickstarts, you'll want at least the A500 and A4000 (or 1200) ROMs (1.3 and 3.0). If you use the Cloanto ROMS make sure you also copy the rom.key to the Kickstarts dir.
You need to get the SKick package from Aminet and install the *.RTB files from it into DEVS:Kickstarts too.
Install WHDLoad, you really only need the user binaries unless youre going to make your own installs, then get WHDLoad-dev.
Thats basically it. Run any installers you want and stick in the game disk when asked. I dont see how it could be messed up if you follow the instructions. It took me less than 5 minutes to install WHDLoad and a few games.
What does your Kickstart dir look like?