Dear Schmirre,
If I understood well your question, I'd say that you need to activate the effect of waves in Sisyphe (EFFECT OF WAVES = YES).
This allows you to account for the wave effects when solving sediment transport rates. Please be aware of the sediment transport formula that your are using and consider to adopt one of the formulas developed for accounting the wave effect, such as Bijker, Bailard or Dibajnia & Watanabe.
I hope it helps,
Best wishes,
Pablo