BeerSmith does have Common Cider and Apfelwein categories to use when creating recipes.
I created an ingredient view for each cider or juice that I've used. Just take an SG reading of the unfermented juice and enter it in the appropriate field. I can't remember the details as I don't have BeerSmith in front of me at work, but it only took me a few minutes to figure it out.
Once you have the data for your juice or cider saved, just enter it into your recipe as usual.
Primary/Secondary: #109 Rye, #110 APA
Kegged: #106 American Wheat, #107 IPA, #108 Nut Brown
Planned: Red IPA, American Brown