Complex sentence: Rather than pay stores a slotting fee, which his start-up company could not afford, he paid stores in yogurt rather than in cash to stock his wares, and also negotiated to pay off the slotting fees over time as the yogurt sold.
Split into simpler sentences: Rather than pay stores a slotting fee, which his start-up company could not afford, he paid stores in yogurt rather than in cash to stock his wares. He also negotiated to pay off the slotting fees over time as the yogurt sold.