The OpenSprinkler firmware supports ‘repeating’ start times, which you can use for cycle and soak. Specifically, instead of setting a program to run for 1 hour straight, you can set it to run for 15 minutes each and repeat 3 times, so the total water time is still 1 hour but split over four 15-minute sessions. I understand that you want to cycle and soak only a subset of the stations. At the moment the best way is to split them into two programs as you said. With the upcoming firmware 2.1.6 there shouldn’t be any problem because 2.1.6 uses a queue-based scheduling algorithm, which allows the same station to appear multiple times in the queue.
To change the program data structure to support any arbitrary station orders and replications is a much more difficult task. This requires completely changing the program structure. Unfortunately this is not something we can do right away.