stelaras1 More likely the 1st option would be better in terms of light gathering
You may not have a choice.
(1) The light path from the telescope's optics to the guide camera's sensor must be the same optical distance as the light path to your main camera sensor. For your case 2 for example, you may need extra spacing for your guide camera. And don't forget, you would need a much larger prism too.
(2) Depending on the optical configuration of the telescope and the size of your filter, the distance of the filter drawer to the main camera sensor may matter (vignetting). If the filter is much larger than the main sensor, it does not matter. Otherwise, if the light rays are converging to the main sensor (e.g., no reducer, not Petzval telescope, etc), you want the filter to be closer to the main sensor, but if you have a flattener/reducer that is smaller than the main camera sensor, then you want the filter to be closer to the reducer end. Just draw the rays out, using the data from the telescope and camera manufacturers.
Be forewarned that in both of your cases, you will need to refocus the guide camera relative to main camera's focus, if you change filters that don't all have the same glass thickness.
Chen