This only works on iOS right now.

Setup:

Modify iosBundleIdentifier in flutter_module/pubspec.yaml to be something unique
cd flutter_module (from the top level) and run flutter build ios, this will create some files that are needed for the integration, don't worry when it fails
Open JuceFlutter.jucer and export for iOS, close Xcode if it opens
cd Builds/iOS (from the top level) and create a symlink to the Podfile: ln -s ../../Podfile (you will need to do this any time you delete the Builds folder)
Run pod install from Builds/iOS to create an .xcworkspace containing the required Flutter bits along with the JUCE code

Running:

Open JuceFlutter.xcworkspace (not .xcproj) and build as usual to a connected iOS device
If you want to use the Flutter debug console, run flutter attach to connect to the running instance of the app

If you modify the Projucer project and export again, you will need to run pod install again after exporting.