Due to a one time capital gain I now believe it will be better for me to file married separately but I have already e-filed my joint return and it has been accepted. Can I amend to separate if done before Apr 16 and if so how do I handle EFT already scheduled.
Yes, you can amend your return to change your filing status to Married Filing Separate. Amended returns have to be printed and mailed in and take up to 16 weeks to be processed so filing by April 16th will not make any difference. If you have scheduled a tax payment through EFT, it will be processed before IRS processes the amended return.
If you have already e-filed your return, then you will need to wait until the IRS has either accepted or rejected that return before you can amend it to make any changes.
If they reject it, then just make the needed changes and re-submit the return.
If accepted, and you are expecting a refund, wait until you have received your refund, then you can go here and get instructions for amending that return.
One important note: Before you start the process of amending the return in TurboTax, be sure you have printed a copy of your original return or have saved a PDF copy to your computer.