Mostly you can 'tell' the other to do something. So when playing as Caddoc and there's something that needs lighting with a fire arrow, when you stand near to it you can press B and he'll ask E'lara do do so, which she automatically does.
Another puzzle did require you to play as E'lara, but then they made sure there was one of those changing spots right there.
Long story short: you don't miss anything in single player - as far as I know.
