Here is what I'd do, now that does not make it correct just because I said it.
First I'd want to get my hands on some sheet music. Hopefully some fake chord or lead sheet music that will show the chord name used over the lyrics. Tie the chord changes to a lyric word -- so you can anticipate when to change chords.
Then as long as they are singing/playing over one chord you will use your bass riff, let's just keep it simple and say you have decided to use a R-5 tied to the clap rhythm. When the song moves on to another chord you move your R-5 to the new chord. In that song you posted I'd be playing a simple R-5 through out the entire song. Changing the root when the chord progression moves to another chord.
Don't worry about a R-5 not being enough to "fill the spaces". Listen to Nora Jones singing
Cold, Cold Heart. The bass is using one 5 note riff through out the entire song.
http://www.youtube.com/watch?v=g35zS1tVO3o
Have fun.