The key difference between the initial retainer payment and hourly rates is that the former is required for opening your file and the latter is the method by which you are charged for work completed on your file. As your initial retainer payment nears depletion, you will be asked to replenish your trust funds by making a further retainer payment.
You may think of retainer payments as credits, or cash inflows into your trust account, and hourly rates as debits, or cash outflows from your trust account to pay for work completed on your matter.