how to know the precedure of solving a actural bio problem? like interface design?

hi 

im a doctorial student in the learning process of rosetta scripts

and i was to solve a problem like i got to design a protein complex A0_B0 with known structure and known complex of A1_B1 A2_B2 all Bi are homologs

i need to design a binder A0 that binds to B0

but I just dont know how

and a teacher told me that i needed to manually docking B0 to like a1

and to use fastdesign,fastrelax, to use taskops of layerdesign,limitaromachi2,PruneBuriedUnsats,and filters like BuriedUnsatHbonds

so how am i supossed to know which mover and taskop to use if i am learning by materials and all myself

is that just experience or ?

what if i am to design a denovo binder or to do structure prediction

what combinations of movers and taskops then? ( assume i know all the meaning of single ones)