I believe that feature went away since Media 100HD now has unlimited video layers. How would it know which one to choose?
I'm a little fuzzy on what you are trying to do, but you can use the bin browser to pick any clip you want to composite with Boris. You need to think Boris is more like a compositor in the timeline, rather than the way it use to be. So you'd need to bring in all of your elements from bins, files, etc,- timeline is a place holder, not where you will get your media from. Make sense?