Jason,
I work on a Mac and, in general, I setup mappings for each of my applications.
If I have an application in my cf web root called "myapp". I would setup the
mapping as:
mapping: /myapp
path: /Applications/JRun4/servers/cfusion/cfusion-ear/cfusion-war/myapp/
As you can tell from my path, I installed CFMX (7.0.2.x) on top of JRun4 (so
it's a little more contorted to get to my cf web root directory).
In my cf code, I would call the cfc like this:
<cfscript>
objMyCfc = createObject("component","myapp.MyCfc");
objMyCfc.init();//etc.
</cfscript>
I've not had any problems using CFCs (and I use them in every application).
Hope this helps!
Craig