Vega 6.6 is only supported using .Net 1.1.4322. You should be able to install .Net 2.0 on the servers but will have to set the Touchpaper virtual directories to use .NET 1.14322 if you are using Touchpaper Services Applications. This can be done by right clicking on the virtual directory in IIS and click properties, then select the ASP.NET tab and set the ASP.NET version to 1.1.4322)
You will need to create separate application pools as you cannot have different versions of ASP.NET running under the same app pool.
If you are NOT using the following Touchpaper Services applications you should be able to install .Net 2.0 without any additional configuration - Touchpaper Services, NMS, SupportMe, Query Tool, ServicePortal, Mobile Portal, Asset Manager and Active Assistance, SurveyCenter.