Permalinks acting crazy

Problem with permalinks.

I have http://www.dubbspotrecords.com permalinks set up with no problems. A webconfig exists in the root for the permalink change. This has it’s own install of wordpress.

I also have http://wdsrradio.com set up under the same host in it’s own folder. Root (dubbspotrecords.com) > root folder > wdsrradio. Within wdsrradio folder I have a separate wordpress install with it’s own database.

Problem:

When I change permalinks in wdsrradio.com, it breaks my whole site with a 500 error. I change it back to default permalinks, everything is fine.

I’m on a godaddy window hosted server. I have the ability to add as many domain names as I want under this plan. Which is why I have a second install of wordpress with a separate domain name.

I already know that I cannot use the same web.config file in the root in the wdsrradio folder. I’ve read that the root has it’s own web.config and the wdsrradio folder should have it’s own web.config.

I guess what I am looking for is the information that needs to be added to the web.config in the root to make the web.config in the wdsrradio folder work.

I just cannot figure out why it’s breaking my site. And I don’t want to use the default permalink structure because it’s not good for seo. And I did change the wordpress url within wordpress to wdsrradio.com and not dubbspotrecords.com/wdsrradio….

Do I need to add a variable to the existing web.config file in the root to let it be known that wdsrradio is a separate install of wordpress?

or

Do I need to add a variable to the web.config that’s in the wdsrradio folder with the separate wordpress install?

I obviously do not know what the variable is. I just want to be able to have both sites dubbspotrecords.com and wdsrradio.com permalinks working for good seo.

dubbspotrecords.com works fine and has a web.config

wdsrradio.com will break with a 500 error if I change the permalink structure from any other than default.

I read somewhere to put index.php in front of the custom permalink. I do not want that. I want all links to be wdsrradio.com/postname.

If anyone has experienced this, please address it with a link that has some step by step to fix this or any other resources to fix it.

Things to remember:

Two separate wordpress installs (one root, one root folder).
Both wordpress have their own databases but under the same host.
Web.config and permalinks works in wordpress in root.
Web.config breaks site in root folder (wdsrradio).