In Wowza Streaming Engine has two options for accelerating encoding, QuickSync and NVENC. CUDA is not used to accelerate encoding in Wowza at this time.
The 4.6.0 release notes explain that in 4.6.0 you can now use CUDA for video scaling, where normally it is done on the CPU.
To do this, open a Transcoder Template, and then under the Decoder choose CUDA.
More info regarding the Transcoder and using CUDA acceleration.