Do you mean the covers on the roof to allow installation of the roof rails, or the caps on the roof rails that cover the connecting points after the roof rails are installed? I'm not sure I see a reason to remove the caps after the roof rails are installed, unless you want to uninstall the roof rails.
You need the type of cross bars designed for roof rails, as opposed to flush fit. These will have straps that wrap around the roof rail to attach the cross bar. I believe Thule 7503 is the correct size/type for the DS (you can verify on their website). I know others have used Rola's designed for a BMW that seem to work as well. Do a search for roof rails/cross bars and you should be able to find more info.