I got it right away. Payment was pending for sometime, but once it went through, I got the PDF saying that the application was received with the EE number as my application number.
But it was very stressful as I had failed payment once. If the system had taken longer time to recognize a failed payment (as credit card identified it as a fraudulent transaction), I would have lost the bus. Thankfully it let me submit again in a hour or two. I would suggest one week buffer unless you have compelling reason to submit it later.