If the JARs are in the classpath, the classes are just as accessible as any standard platform class like java.util.Map. I give a demonstration here, where I explain the custom interface I built so I could sometimes use the same code on both platforms: http://rocketnia.wordpress.com/2010/06/01/lathes-arc-to-impl...
Since then, Jarc's actually added Rainbow compatibility functions, so you might be able to get away with writing code just for Rainbow without leaving Jarc too far behind. Rainbow's faster, but Jarc has a more straightforward implementation.
I recommend having one of the JARs be a language with eval, like Groovy, JRuby, or Clojure. Jarc and Rainbow convert certain values to/from Arc in ways that are nice most of the time but sometimes lose precision, like the distinction between Boolean.FALSE and null.
