Everyone is entitled to change his or her mind now and again, but if your contractor has already started the job, it's best to keep your ideas to yourself.
Adding an additional level to your under-construction deck may seem like a good idea, but changing directions in the middle of a job can really cost you. Not only will you have to pay for the additional labor and supplies, you're also going to have to shell out for adjustments to the work you already paid for. For example, that deck will have to be torn down and rebuilt to hold the additional weight. Before you sign the contract, make sure you're getting what you really want (or at least something you can live with); otherwise, you'll be banging your head against a newly rebuilt brick wall when you get the bill.
If you decide to move forward with a new plan, ask your contractor for an estimate. Once you've got a written document detailing what changes need to be made, how long they'll take, and what the entire process will end up costing, you might decide to forgo any of those spur-of-the-moment revisions. And if you do decide to renovate your renovations, at least there won't be any surprises.