The penultimate day of the 30 days of After Effects series is a great workflow overview that dives a bit deeper into some details, which all deal with combining 2D and 3D together in After Effects.
School of Motion’s Joey Korenman has a look at bringing 3D objects into Ae using the Cineware plugin link and also walks through some higher level compositing concepts.
These include working with muti-layer EXR files, making use of render passes, or cinema 4D object buffers / motion vector passes, and how to get After Effects native 3D layers to synchronize with 3D renders.
Check out the tutorial for combining 2D and 3D elements in After Effects here.
