JWM: You are not wrong. It's basically an old school X window manager that you configure through modifying it's config file and .Xresources, .xinitrc, etc. Sure, it's not as easy as a built-in "preferences/settings" widget, but I think for the basics that are in .jwmrc it would easy/feasible/trivial to create one. It's XML so by definition, it's well formed. There are standard X tools like xfontsel, probably color pickers that could be pulled in.
So it's not really a problem, it's part of the distinction between a "Window Manager" and a "Desktop Environment"
CTWM: go to the homepage and it talks about themes. Looking at what is "a theme" you see it's the .ctwmrc config file, .xinitrc to start things and any custom images/icons. One could easily do something similar for jwm.
teo : would you be willing to post your .jwmrc? Your tray configuration looks interesting. I'm assuming the icons on the left side are "click to launch an application" like terminal, web browser?