You need to run the deployment wizard from AX client (Administration->Setup->Internet->Enterprise Portal->Manage Deployments) on the web server to deploy the site defintiion and other files.
Refer to the step by step implementation guide
If you have followed this and still don’t see the site defintion, then there is KB Article on this.
The file copy operation of the WSS templates may fail for several reasons including the following; the current user account does not have rights to the file location; the current server has both Windows SharePoint Services 2.0 and 3.0 installed on the same machine and the 3.0 version cannot be determined; the Windows SharePoint Services installation has additional language packs installed.
Manually copy the following files:
Copy the file WEBTEMPAXSITEDEF.XML to the following folders:
%ProgramFiles%\Common Files\Microsoft Shared\Web server extensions\12\TEMPLATE\SiteTemplates\XML
%ProgramFiles%\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\1033\XML
Copy the AXSITEDEF folder
%ProgramFiles%\Common Files\Microsoft Shared\web server extensions\12\TEMPLATE\1033
%ProgramFiles% is a variable and is used for your windows Program Files folder, e.g.
After making these changes the templates should be visible in SharePoint Central Administration when creating a new site collection.
Note: On non US-English installations you may have more than the 1033 folder which represents the Windows SharePoint Services language ID. You will need to copy the same files to the other localizations as you did to the 1033 folder.