Get a big pair of comfy headphones, one that you can wear for hours, and put them on whenever you don't want to be bothered. You don't even have to listen to music, they're just there to signal that you're not to be bothered. If someone does bother you, pull one side off, say you're busy, send an email or come back after X-o'clock. Wait for an acknowledgement then pull the ear cup back and go back to work.

Only break protocol for your boss's boss, even then only accept one sentence from him, give one sentence back, and unless the office is on fire say you're deep into Y and you'll stop by later to discuss. When you do stop by, make sure to mention that interrupting you like he did is not pleasant and request he use Slack or whatever instant messager your company uses.

Your boss can just learn to use email. It may take a few discussions before he'll respect it but it'll be worth it. Send anyone who complains a link to Paul Graham's Maker's Schedule, Manager's Schedule.