1.Create new application pool in IIS6.0.
2. assign Asp.Net runtime 2.0 to newly loaded asp.net 2.0 web application domains.
3. load this application domains to get server in newly created application pool.
4. Don't try to assign application pool serverd by 1.1 process to 2.0.
5. one application pool one version of asp process.
Satalaj