Certainly, I would recommend taking the "abstract analysis" course first. It will definitely help you in taking the "linear analysis" course later. (Remembering that the best thing you can do is talk to the faculty who actually teach the courses for their recomendations!)
As to how much use they are in "Applied Mathematics", that depends strongly on what you mean by "applied mathematics"- an unfortunately vague term! Some people use "applied mathematics" to mean the theory behind the kind of mathematics used in applications. Certainly, if you consider yourself a mathematician of any sort you should have as much anaysis as possible. Functional Analysis (what, I think, is your "linear analysis") is used in developing the theories behind solution methods for differential equations, among other things, but are not really necessary just for using those methods. Again, think about exactly what YOU want to do and talk to the faculty.