There have been cases where projects have blended PEGA methodology with more traditional development approaches such as Agile or Waterfall. Normally this is done based on dependencies. For eg. large J2EE changes would follow waterfall, smaller J2EE changes follow Agile, ESB changes would follow RUP, Pega would follow Smart BPM- this is just an example and it depends upon the project decisions.
In these cases, there are many challenges for various development approaches to match up the timeline: