You should be able to change Slit behavior in the Fluxbox Options Menu. Take a look at the manual
You can also change the settings in your .fluxbox/init file. You can try setting session.screen0.toolbar.onTop to false, or session.screen0.slit.autoHide to true. The first one will let you have windows over the slit, the other one will only show it if you move the Mouse to the edge of the screen where the dockapps are.