To file a state return as Married Filing Separate, you need to create a Federal Return as Married Filing Separate. This Federal return is just for informational purposes only.
Once you have created the Married Filing Separate Federal Return, then you create the West Virginia return from that information.
If you are using TurboTax online you will need to set up a separate account to create the Married Filing Separate return, or you can use the Desktop Version of TurboTax where you can create up to 5 Federal returns at no additional cost.
If you need to file a Joint federal and separate state returns
Reading the FAQ it looks like you have to use 3 accounts. One to file the Joint return. Then you each need another account to fill out fake federal MFS returns to do your separate state returns. So you will have to PAY for 3 online accounts (3 federal returns and 2 state returns). That's why it's cheaper to use the Desktop installed program. If you don't have a computer to install the desktop program on maybe it would be cheaper and easier to go to a local accountant or tax place.