Even though the latest version of ASP.NET is 2.0, but in many cases we’d like to host both ASP.NET 1.1 and 2.0 web applications on the same physical IIS Server. It is doable, but we will need to put all 2.0 application in a Application Pool, and ASP.NET 1.1 application in another Application Pool.

By default, all IIS 6.0 web applications belong to a single application pool called default application pool, but we can partition the applications based on the following steps:

Use the ASP.NET tab in the Internet Service Manager
to make sure the 2.0 and 1.1 apps are targeting the intended
version of the .Net Framework.

Also, you need to have 1.1 apps and 2.0 apps in different Application Pools.

Use the ISM to create a separate Application Pool for 1.1 apps
( or perhaps a separate one for 2.0 apps, depending on your original configuration )
and make sure that 1.1 Apps and 2.0 apps are assigned to separate Application Pools.

You can have as many Applications Pools as the number of Applications you have,
but remember that each AppPool takes up memory resources.

At the very least, lump all 1.1 apps in one AppPool,
and all 2.0 Apps in a separate AppPool.