You should use the project module to achieve this. Your items should be entered as project item requirements and your billing should be done throug on account transactions on the project.
If you attach a payment schedule to your sales order with a total value of 10000$, 40% or 4000$ will become due on the day you specify through the payment schedule, the other 40% will become due at the second date specified through the payment schedule and so on. So, actually AX2009 can actually handle the situation.
You might also want to take a look at the project module billing features.