Hello. You mean to have different template for quote and different for invoice? That can be possible, but it would be probably needed to be done as paid support. If I understand, quote is only different document for same order.
But there is current problem with VirtueMart (some users requested it already), that it does not suport payment (e.g. by paypal) of already placed orders. It only supports payment in time of placing order, at least with default installation. Maybe there are som plugins that supports payment after order was created (e.g. if created by admin), but we don't know about them.
As for integration with VM, we will think about that.