When you run Microsoft Dynamics Ax 2009 EP setup and go through the setup wizard, you might wonder what is going on behind the sceens. Here is a high level flow

Set BCProxyAccount Info in DynamicsAX ( from the user Account info entered for BC proxy in the Setup screen)
If(VirtualServerIsAlreadyExtended)
{
           Get AppPoolAccount From IIS
           if (ConfigureForWSS check box is checked in the setup screen)
           {
                        If (ApppPoolAccount in IIS  == BCProxyAccount in Ax)
                       {
                                  Set password entered in setup screen for BC Proxy to the  AppPool in IIS

                        }
                         else
                        {
                                   ConfigureVirtualServerWithNewApplicationPool ( use the BC proxy account and password entered in setup screen for the
                                   new app  pool)
                           }
                         Configure AuthenticationMode to NTLM
            }
            else
            {
                       If (appppoolaccount <> BCProxyAccount)
                                  Log Error
            }
else
{
         Extend VirtualServer In Sharepoint
         ConfigureAuthenticationMode to NTLM
} 
Remove Old WebPart Package
deploy EP OnS harepoint
       - deploy Static Files
       - deploy Web Controls
       - deploy All Web Parts
       - add EP Site Definitions
       - add/remove Site Templates
       - install Feature - Ax Search Feature
       - install Feature - EP Feature
       - if(MOSS Installed)
                    install Feature - Ax EP MOSS Feature
        - install Feature - Ax EP DataConnection Feature
        -  Create Install Information File
        - Integrate EP Help

if (Reset IIS Option is checked)
{
       Do IISReset
}

Upgrade Sites To DAX 2009  ( from DAX4.0)
Create Install Information File
Add Performance Counters
if (CreateWebSite Pption is checked)
            Create EP Site ( if bcproxy account is same as app pool account and IIS reset is checked)