Paid for lawn to be completely aerated, seeded and fertilized- company botched job- what do I pay him?

You have a contract with the company. And BOTH of you have responsibilities under that contract. In the written contract, was there a guarantee that the seeds would grow? Was there a guarantee that the weeds would be gone. Or did it simply state that they would do certain things which they did? Even if things aren't as promised, you must give the company reasonable opportunities to fix it themselves. As things stand at the moment, you owe them the full amount due...with or without an invoice.