No, using the non-filer option to submit your direct deposit information should not mess up your stimulus payment. The IRS will use your social security number to process your payment. Since you have filed a 2019 return, they will go by that information.
What if I accidentally filed as a non filer? how do I tell the government it was a mistake and am I allowed to still file my taxes?
its not allowing me to finish my transmission because its saying Ive already filed under the same Social Security Number
When you filed as a non-filer, what you did was file a return with no income. Because you already filed a return, your actual tax return e-file was rejected - you can't file more than one tax return per tax ID #. You will need to file an amended return for your 2019 taxes, which will require you to print and mail the return, as amended returns cannot be e-filed. That's how you tell the government it was a mistake. To file a 2019 Amended return click on: How to amend (change or correct) a return you already filed