No, it will not be proportional. Every CC company that I'm aware of inserts language into the agreements indicating that your payment will go towards paying off balances with the lowest interest rate first.
Lets say you put a balance of $10,000 on a card, with 0% interest for 1 year. Then you buy $5,000 worth of stuff and your regular rate is 12%, so you have a total balance of $15,000. Then, lets say you pay $5,000 toward the balance. What you'd end up with is:
$5000 balance at 0% for 1 year (or whatever remains of that year), and $5,000 balance that will incur interest charges at 12%.
That's how they like to trap you with those balance transfers. Once you put that balance on your card (and get 0% for a year or whatever deal), you should put that card away and not use it at all. Pay off the balance as fast as you can, but do not add any other purchases.