Cue_or_GDI_to_CHD.7z
Unzip those 2 files into your Dreamcast roms folder and run the bat, it will create a chd of all the games in a the folder, and will leave the originals as well for safety, once you are happy that the chd's work OK you can delete the old files, i believe that your games need to all be unzipped first though.
As for disc swapping i havent got that far into any games to see myself, but you can bring up the redream UI with the guide button, so im guessing you just pull that up and select the other disc. You would need to give redream your rompath in the UI so it can scan your games folder.