With TurboTax Online you pay per return. If you prepared your tax returns together, when you get to the payment section you will be prompted to make one payment that pays for both returns. You will pay the regular fee for yours of $59.99, plus an additional $19.99 for your spouse.
If you didn't prepare your returns together and wish to, you'll have to start a new return using TurboTax Online Self-Employed and be sure to choose to "prepare your returns at the same time".
Turbotax is charging me the full rate for self-employed on both mine and my wife's return (filing together), but she just has a simple T4 and a couple of RRSP contributions.... is something wrong??