The Tiffen 2.0 filters are a substantial improvement over the 1.0 version. They allow multiple layers and individual layer "transparency" control. My current workflow involves keeping layers of my favorite filters up in the "Effect" pane. I keep them turned off but can quickly turn them on without having to wade through the filter selection hierarchy (which I'm sure is clear if you shoot with a lot of real physical lens filters, but isn't the point of this package that you shoot first and filter later?).
BTW Version 2.0 is a bit crash-happy on OSX 10.5.5, but I'm getting in the habit of doing a quick save before calling up the filters.