I installed Mobile Joomla and the site came up without any of the colors of the template I use.  I went into the .css file for iPhone (which is what I am currently viewing it on) and changed the background from pinstripe to the color of my template but this still did not make a difference.  

There doesn't seem to be anything in the settings to control the actual look of the mobile website. 

What am I missing here?

MJ includes few demo templates, it doesn't transform your desktop template into mobile one. Just adjust styles of demo template, or get another one.