I am running IIS on Microsoft OS and I would like to know how could I use several ACO for the Web Agent installed on it?
As Web Agent cannot run outside the IIS process, and the IIS architecture (6 and 7) does not allow to run multiple IIS instances on the same machine. That is why you will have only 1 ACO per IIS instance and because of Microsoft limitation, you will get only 1 IIS instance by machine. You may consider to use Apache which allow you to launch several instances.
This has been enhanced since Web Agent 12.52 SP1 CR04.
Snippets from the Web Agent New Features in the Additional Information link.
From 12.52 SP1 CR04, Web Agent supports independent agent configurations for application pools and their websites for Microsoft IIS Server. CA Single Sign-On provides a separate Web Agent configuration file for each application pool in your environment; this lets you configure different settings for different application pools and their websites.
Web Agent New Features > Support for Multiple Agent Configurations for Application Pools