well the best of all worlds is if you have ODN and access to all the programs toon uses otherwise I believe it installs shareware versions needed to get it to work. So I guess 1st off what apps do you have and what versions.
Don't think you probs are because of needing WB4. Sidebar not showing sounds like Desktop x not running or loading it, you dont mention does the top bar show? If it does but side bar doesnt dx is running so you might try going to desktopx and select load and browse and reapply the cartoonbars.
Anyway make sure DesktopX is running then the side bar may appear and to change color make sure under Display -> Appearance that you Select "Cartoon Short color custom" and then click on the color box and make sure that enable coloring is checked. If its set to toon short then even if you check enable coloring and select one it wont apply. (If this is something your only able to do with WB4 I didnt realize and appologize)
If already done all this sorry, just trying to help
Just Jess