What I have read about applying this pre emergent poison is that it goes on the soil, not on shrub branches.

Steve, the challenge with this situation is that your pre-emergent needs to reach the soil surface at a certain rate of application. The chemical needs to be watered in properly in order that the solids can liquify, enter the soil, and form a temperary barrier against germinating seeds.

Applying the granules over the juniper and hoping that it gets to the soil in a relatively even layer is not the best use of Preen.

There are other options, but I would first need to know what kind of weeds you're battling with.

For example, I have a dense growth of beautiful Parsoni juniper in our front beds. Few weeds are able to infiltrate but we always end up with a crop of nutgrass and a few broad leaf weeds. We are able to spray a mist of herbicide that kills grassy weeds but we pull the broadleaf weeds. Preen (or similar) is not an option.

Those weeds you have are probably perennial and continue to grow from their roots after you try and pull them. Preen works by not letting seeds grow and your situation is probably past that point. What weeds are you dealing with? Grasses?

I have the same problem with my juniper. It has been infested with nutsedge and I cannot find a product that will kill the nutsedge but not the juniper. Does anyone have a solution to this problem?