The RUP is a software develoment process that can be implemented for any platform. The Rational tools can be used to develop software within the framework of the Unified Process. The major issue for an iSeries shop is that these tools do not run on the iSeries and are Object Oriented. If your develeopers are still maintaining monolithic applications in RPG III, then you are attempting to jump 15 years of architectural evolution in a single bound. Good luck.
Rational Method Composer (RMC) allows you to customize the process, I would strongly advise configuring a lightweight process using Requisite Pro for requirements management, Clear Case LT for change management, Clear Quest for issue tracking and RSA for business modeling.
If you have already made the move to JAVA, then these tools will provide a dramatic improvement in your software development process.
If you are still RPG, then you have the cart before the horse, you will have difficulty mapping an OO design to structured programming.
If you want to succeed you will need consultants to guide the modernization. IBM has some good Rational folks that have helped our iSeries developers retool.
I hope this helps. . .