EXTJS MVC (Sencha CMD) and PHP MVC Framework not playing nice

I can't seem to figure out how to have EXTJS MVC with sencha cmd work with an MVC PHP application.

It seems like the routing at the PHP application level breaks the extjs MVC.

E.g.

/app/controller

/app/model

/app/view

/system

/web/myapp (extjs mvc app)
/web/js

/web/images

/web/css

For example,

www.mysite.com/crm

This would hit the crm controller which would them take me to a view specified by the controller. But the page root would be /crm in the browser. This breaks all the paths that extjs looks for the files in since extjs is expecting the path to the /myapp

What would I change in the bootstrap.json file or app.json file to make this work. I've tried lots of different things and they all break the builds. "sencha app build -c production"

Even copying the output from index.html that's created by the builder with the microloader and putting that into into my view file doesn't work. That ends up with bad paths too.

Anyway, so the question is, with an MVC app, how do i make it work when my server-side mvc is doing the routing?

Is there something i should be modifying in the app.json that will make the build not use relative paths?