I finally got an answer back from my planner about this. Wanted to answer the question for any future brides.
$1,000 from your deposit does count towards your minimum expenditure. So if your minimum expenditure is $10,000 and you already paid your $2,000 deposit then all you owe at 90-days is $9,000.
Also, there is a Wedding Payment Form that your planner should give you. You may have to ask for it. I certainly had not received it and they acted as though I should already have it. So check up on this if you didn't get it.
There are many options to pay with including credit card with a form you fax back to them, personal check, money order, cashiers check or wire transfer.
Hope that helps future brides!