I was able to set up the commerce site as a child application of the cms site.  I needed to update the web.config for the cms site to add  <location path="." inheritInChildApplications="false"> around the sections that cause problems if inherited by the commerce application.  I basically just added it around all the sections so as to have a clean web.config file, though that could be streamlined in the future.  The issue I am having now is that commerce is trying to access a specific port to download resources, as opposed to using the path straight.  My style urls look like the following:

http://domain.com:port/commerce/...

Instead of:
http://domain.com/commerce

More information about this issue is that it seems when making a request to commerce, it is returning the port in the result of the url instead of just the url that I have set up.

http://www.domain.com --> Main cms (runs on port 8012)
http://www.domain.com/commerce -> Commerce Manager

Resources that are running from the Commerce Manager page like css files are loading as
http://www.domain.com:8012/commerce

The issue is that this is going through a load balancer that is sending requests to this domain to port:80 automatically and it maps it to our local servers that run off port 8012, so commerce ends up looking for a load balancer site on port :8012 that doesn't exist.

Any ideas on how to make commerce return urls without the port?