Ha, I might have the perfect solution for you!

To sum up:
- You can't run at the system level (or even if you could, don't do it,
it's less flexible and more cumbersome to set up).
- If you redefine a keymap from scratch, you need to use xkbcomp, not
setxkbmap!
- If you only want to change some modifiers / options over a system
keymap, you can use a combination of setxkbmap and xmodmap.

See my dotfiles for an example:

	https://github.com/ambrevar/dotfiles

In .xkb, I have defined a new "usim" keymap.  The *.xkb file and the
symbols subfoler are mandatory.

To load the map, I call the following from `.xprofile`:

	xkbcomp -I"$HOME/.xkb" "$HOME/.xkb/usim.xkb" $DISPLAY 2>/dev/null

I have more settings:

	setxkbmap -layout us -variant ""

This resets the keymaps, it's useful when I do some live changes to my
keymap and they I can revert everything by simply sourcing `.xprofile`.

	xcape -e 'Control_L=Escape'

Make Left Control (which is Caps Lock in my keymap) act as Escape when
not used as a modifier.

	numlockx on

Turn on the numpad by default.

	xbindkeys

Set additional keybindings such as the multimedia bindings as par the
`.xbindkeysrc` file.

Hope that helps!

-- 
Pierre Neidhardt