Most slicers require the different parts as own files with synchronized object axis. Design both parts in place so they match how they need to be printed.
Depending on the design software you use you select a part that you want to print in material A and export it, then you export the part you want to print in material B.
Then in the slicing software you assign extruders/materials to parts. In Simplify 3D you add the object you want to print in Material A to the process that uses Material A, then assign the object you want to print in material B to the process that uses material B. When preparing to print select the two processes needed.
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