If you're out of undergrad and working, I think you should avoid asking a professor to write a recommendation letter. It seems that adcoms prefer recommendations from the working world rather than from academia. And yes, you are right, asking a current manager for a rec letter is pretty much telling them you plan to resign to go to school, so you should have that conversation before asking for the letter. If you're not ready to tell your boss/employer that you're applying to school there are plenty of alternative recommenders - former bosses, clients, customers, people from one of your ECs, etc. I believe there are a number of people here who successfully applied without having their current supervisor write a recommendation or know that they were applying.