Contrapuntal techniques can be applied to more complex rhythms. When you start learning counterpoint on its own (especially from Fux) it might be hard to see how the techniques apply to the pieces you want to write. One trick is to make sure you understand nonharmonic tones, or ways of creating melodic motion in a tonal context. I don't have time right now to give examples on staff paper, but some terms to know are accented (occurring on the beat or on a strong beat), unaccented (occurring off the beat or on a weak beat), auxiliary tone, passing tone, neighbor tone, incomplete neighbor, double neighbor, anticipation (or portamento if you're working in a sixteenth century style), suspension, retardation, escape tone, pedal point or pedal tone, consonant leap, arpeggiation, appogiatura, enclosure, nota cambiata...