Hey Daniel,
all you should need is an Apache rewrite to the effect of:
if URL matches mobile version pattern, add ?useskin=mobile (or whatever your skin is called) to the query and run that against the "desktop" version.
So, assuming the "desktop" site is:
muppet.wikia.com
and the mobile site is:
m.muppet.wikia.com
Going to m.muppet.wikia.com/wiki/Main_Page rewrites to muppet.wikia.com/wiki/Main_Page?useskin=mobile
You can also use user agent detection instead of URL matching, which is what we do.
This is a simplification of our approach (which involves some a combination of headers and php skin fiddling), but should be enough for most basic installations. Give it a try and let me know how it goes.