Just to share, As my HLE is expiring next month, I called HDB to check if I need to re-apply again. The officer mentions that HDB will let me know again when they invite us to take possesion of the flat, and I need not apply now.
The downpayment (5%) will be indicated in the notice letter to sign the Agreement for Lease. I went HDB to sign the Agreement today and they only deduct 5% for the downpayment. After which, they will wipe out our CPF when we collect our keys. (By the way, I'm a first time buyer as well).
You may wish to confirm with (call) HDB that they have received your docs, and are processing it. The status will be reflected online (MyHDB) when it is approved.