On recent IOS-XE code (17.3) you can do both and many customers are. The way I like to think about it is that Cisco DNA Assurance is used for isolating and troubleshooting everyday problems on the network (onboarding, poor performance, connectivity) and Stealthwatch is used for learning of possible security issues on the network (such as suspicious traffic flows). Cisco DNA has a Stealthwatch workflow that will help configure the necessary netflow and embedded traffic analytics configs for the switches to export the necessary data to the Stealthwatch flow collector. Here is a pretty good and short video showing it in action.
https://www.youtube.com/watch?v=PKujAdIoiOU
The video may assume you already have the Stealthwatch credentials defined in Settings->Stealthwatch
