Hi Jaime ,
I don't see a problem with the setup - Sitefinity application and other .NET application. You can crate a new website and put Sitefintiy in its root. Then create a new virtual directory under Sitefinty's website that will host your other .NET application. Here it would be better if both the applications are build on .NET 4.0 . You should also break the applications web.config inheritance.
In some places you need to explicitly use clear
tags to break the inheritance. In most of the cases this happens in handlers section.
the Telerik team
Do you want to have your say in the Sitefinity development roadmap? Do you want to know when a feature you requested is added or when a bug fixed? Explore the Telerik Public Issue Tracking
system and vote to affect the priority of the items