Here I layout a simple method for designing for multi-material FDM/FFF in Fusion 360. This is particularly effective for functional materials (i.e. conductive) and defining specific features (i.e. text) within an object that you want to define as a second material - such as my 3D Printed piano Instructable.
Some more complicated features require the use of the Patch and Sculpt workspaces - I plan to write these Instructables soon, so check my profile!
Anyway, on we go...
Step 1: First Create a New Component
Create a component for your first material. Typically this will be your 'dominant' material, i.e. your most frequently used.
Step 2: Generate Your Geometry for Your Complete Part
Generate the overall shape of the object produced (i.e. irrelevant of material) ensuring the new component is activated.
Step 3: Create a Component for Your Second Material
Activate the top level component in the tree and repeat step 1 for your second material.
Step 4: Generate Your Geometry for Your Second Material
Activate your second component and define your second material's geometry. It is also a good idea at this stage to apply two different appearances to your components to distinguish them.
Step 5: Use Combine to Form Final Shape
Next we activate the first component we made and go to: Modify > Combine. This will enable us to make the geometry for Material 1 separate from Material 2.
Select your body in the component from step 2 as the target body and the body from step 4 as your cutting tool. Select 'Cut' as your operation. SELECT TO KEEP TOOLS.
Step 6: Export STLs, Slice and Print
These components can now be saved as STLs, and exported to slicing software (in my case, Cura). Most slicers have the ability to 'merge' the STLs back into their original relative positions.