Both sentences are ambiguous in their meaning. They imply that the agreement was NOT to make the down payment, whereas I assume you are trying to inform them that there was an agreement, the agreement was to make a down payment, the down payment has not been made, therefore the company has not (yet) met the agreement. If that's the case then I suggest something like this: The agreed down payment has not yet been made by your company. 'Yet' changes the meaning in a very subtle way. I would use 'yet' if you want to express that you are still waiting for and expecting the payment to be made.

Both word orders are OK. The yet is optional; it adds emphasis.

These are all pretty close. There isn't one way to say it. "The down payment that your company agreed to pay has yet to be received." "Per the terms and conditions agreed to by your company, accounting of our records indicated that we have yet to receive receipt of your down payment. Please remit payment for services within 30 days, or per the terms and conditions of the agreement we will be forced to terminate services."