Great question!

When a customer signs up and pays you, a shipment is immediately generated. You can fulfill that shipment at any time, but the order date will be set as the date at which the subscription is created and charged. The customer's second shipment is created ONLY when they are re-charged, and so you will not see any future shipments for their renewals until that renewal occurs.

What happens if someone pre-orders 6 months?

When they pay for the order then every shipment is immediately created with an adjusted order date to reflect the cycle.

What this means is if a customer places an order for a 3-month prepaid subscription on May 24th 2014, the first shipment generated will have an order date of May 24th 2014. The second shipment generated will have an adjusted order date of June 24th 2014 and the final shipment generated will have an adjusted order date of July 24th.