Hi,
if your installation is a CRM 4.0, you can use the ISV folder to host your custom web pages.
If your installation is a CRM 2011, you can't add web pages under the CRM Website, if your pages are client side (means only HTML + JavaScript) you can add them as webresources inside CRM, if it is an ASPNET website, you need to host in a different place (another port as you already did or put in Azure)