It is absolutely OK to have both classic RadControls for ASP.NET and the new RadControls for ASP.NET AJAX ("Prometheus") running in the same web application.
There are two possible problems, that you might encounter, if you are using a classic and an ASP.NET AJAX control on the same page (for example two RadGrids on one page - one classic and one ASP.NET AJAX)
1) If the two controls have skins with the same name, they could interfere with each other, because the CSS classes are the same, but the styles and the HTML output are a little different.
2) You also have to be careful with namespaces in code-behind, since both Telerik.Web.UI and Telerik.WebControls namespaces contain a lot of methods and classes, which have the same names.
Let us know if you stumble upon anything.
the Telerik team