If you already have a SharePoint based intranet portal for your company , you may want to create the Microsoft Dynamics AX Enterprise portal as a sub site to this intranet portal to provide a seamless integrated experience to the users. For EP sub site creation to work, you need to check and make sure the below two are set correctly.
1. The application pool of the IIS Web site running the intranet portal need to use the BC proxy account as the identity
2. In Sub site creation, select the Microsoft Dynamics AX Enterprise Portal Site template and custom tab and also select “Use same permission as the parent site” option for User permissions. ( The SharePoint permission is only the front end gate keeper and actual data visibility and access permission is controlled inside Microsoft Dynamics AX.)