Yeah, that’s a known parameter mismatch (QGC 4.0 doesn’t have full support for ArduSub >= 4.1), but it should still work fine. That said, you can also update to QGC v4.1.6 (our latest recommended version) to fix the warning 
You can check that FRAME_CONFIG is set to Custom, and ensure that the Motors Setup Page is showing all 8 of your motors - I believe when using a custom frame no frame image will appear. From there I’d suggest using the motor test sliders to confirm the motors are all connected to the correct locations, and then you can either set the relevant Reverse checkboxes while doing that, or use the “Auto-Detect Directions” button once the vehicle is in the water (which I believe should work, but may struggle given the less strong alignment of motors in this configuration with each vehicle rotation angle)