Answer: I think you might want to consult with your county extension to obtain a specific diagnosis of the problem that is affecting your junipers, then work from there. They will be able to tell you the best control methods for the specific problem you are seeing. I really think you need to get that first, because if you are seeing a rust colored discoloration it is not cedar apple rust.
In the meantime, here is some information about fungal infections and cedar apple rust on juniper that you may find helpful. Please note the cultural and control suggestions given, you should not really need to be spraying. There are also charts showing resistant varieties.
As far as cedar apple rust, this problem shows on junipers in the spring as very odd looking orange lumps and gelatinous growths with little protrusions -- which can be removed by hand. Here is a photo to help you recognize it.
The "rust" stage of the disease appears only on apples and other susceptible broadleafed plants. Good luck with your junipers!
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