1. Which output should I use and are there any differences between them (Differences such as picture quality)?
Answer: For digital channels, use the component or DVI. No loss in image quality. I have found that using the same connections for non-digital channels results in poor picture quality for this (and apparently most) DVR units. Using S-Video for standard channels results in decent picture quality. Results may vary depending on the type of TV you have. Mine is a DLP.
2. Is the guide visible on all outputs?
Answer: No. Guide is only visible on the digital outputs. I cannot see the guide on my S-Video connection
3. Are all 6208/6412 outputs on at the same time?
Answer: Not sure what you mean, but if you're asking if you have to select the outputs you want to use and "turn them on", then no. All outputs work out of the box so far in my experience.
4. Am I missing out by using the plain old 6208 RF connection?
Answer: Don't know -- probably will depend on what you want and the type of TV you have. For digital, you'll need component or DVI as I don't believe any other connections support digital for most TVs. I do miss having the old RF out from the Moto box, but I can live with not having it. If I need it, I still have composite video out and I can use an audio splitter (in fact I am) with no loss in apparent audio level or quality.