To configure your server instances to use the ATG-Endeca integration, select [3] ATG-Endeca Integration and [4] ATG Commerce in the Product Selection menu:

[1]  ATG Platform and Content Administration :
      Includes, optionally, data warehouse components and Preview
[2]  ATG Site Administration :
      Includes ATG Platform and Content Administration.
[3]  ATG-Endeca Integration :
      Includes ATG Platform. Select this option when Endeca is used. Do not
      select this if you are using ATG Search
[4]  Oracle ATG Web Commerce :
      Includes the ATG platform and ATG Content Administration. Optional:
      data warehouse components, Preview, and Oracle ATG Web Commerce
      Merchandising
[5]  Oracle ATG Commerce Reference Store :
      Includes the ATG platform, ATG-Endeca Integration, ATG Content
      Administration, Site Administration, Oracle ATG Web Commerce, and
      Oracle ATG Web Commerce Merchandising. Optional: data warehouse
      components and Preview

If your installation includes Oracle ATG Commerce Reference Store, you can select [5] Oracle ATG Commerce Reference Store instead. Your servers’ installs will automatically include ATG Commerce and the ATG-Endeca integration, because Commerce Reference Store requires them.