Create a project for the RGB imageset, add RGB images to the project and set the camera type. Save it without processing it. Create another one for NIR similarly to RGB. Create one more project and select project type: "Project merged from existing project" and add the RGB and NIR projects to it. Now you can do full processing.
If the processed RGB and NIR mosaics are not identical, not well aligned, set a couple of manual tie points in the RayCloud editor and process it again.
In the Index Calculator add a new formula for NDVI and use the NIR channel of the NDVI camera and the red channel of the RGB camera.