We recommend that you prepare your returns together so that the software can do any necessary transfers automatically. However, if you want to prepare your returns in different versions of TurboTax, then you would need to prepare your returns separately.
Please also note that different versions of TurboTax Online support different things. If you start a tax return in one version, but enter something that isn't supported, you will need to upgrade your return. Please see these TurboTax FAQs for more information:
Why did I have to upgrade my TurboTax Online edition?
Who can file for free using TurboTax?