Some updated thoughts:
1) I'd keep the [X]'s inside the App to be honest. They look kind of jarring outside, but maybe there is a third option I am missing
2) Still need to move login/signup to somewhere more obvious. Maybe move both those up to the very top right, along with moving "Hello Guest" with them up there as well. Then move the logo to the top left (instead of a little bit down from the top left), and make the Logo, sign in/signup/hello guest into a "top bar" by adding a line below these items. Would probably help a lot.
3)Pay Now is not overlapping, but now I'm not sure what it means. Does this mean I need to register (change this to Sign Up to keep wordage the same) to get the "pay feature", or is this part of the invoice?