I try to think of a harmonic structure I want to work with between each corresponding part.
Then I try to think of building blocks and how to arrange these blocks
My system might work something like this.
A+ (where + is a variation of the main theme)
A+ / B (where / represents layering in this case A on top of B)
C/A+/B (introducing a new motif on top of the existing structure)
Now I run 3 independent looping rigs so it is relatively easy for me to work in this fashion without tripping over myself- I don't know if the RC50 gives you this degree of flexibility.