I went down the BB Ant build script road a year or so ago, got a lot of help on this site, and tried to document my progress on this site. Hopefully the links I place will help you and others.
I have marked this as "community wiki" since it doesn't directly answer the question but I do think it is useful.
Basic algorithm
My answer on this page shows the algorithm for a working build script (BlackBerry: create COD from JAR source file in Ant script). Perhaps this is more complicated than you are looking for, but it does show the relationship I found between javac and rapc.
To summarise, I wanted to include my SDK into the final build, and the steps were:
javac the SDK to create CLASS files
preverify the CLASS files
jar the SDK
Copy the SDK JAR file into the project
javac the project - use the SDK JAR as the classpath
preverify the project CLASS files (again, use the SDK JAR in the classpath)
jar the project - add the SDK JAR as a zipfileset
jarjar this project JAR to refactor package names as required
Finally, run rapc on this JAR - it will find no duplicate COD files & should run fine.
Please read the other answers on that page, since they offer great advice that I used in my end result.
Extra Info & Including a JAR into final output
I'd recommend this page just for the extra links that I included in it - the exact question is unrelated (BlackBerry - Ant script to include JAR in project without external dependancies).
Again, the value is in the answers that the other guys provided.
Misc
Here are a couple of links to other BB build script issues that I had - you or someone may find them useful:
Finally this one speaks to a mistake in the documentation when compiling your own code into a library for import into a different project: