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The rules state that gaps must be fully labeled, what counts as clearly labeled, would something like a sharpie work?

Yes. A sharpie or a sticker label that marks the start and end of the Gap. Helps the supervisor to measure the device.

Put yourself in the ES's shoes. They don't have very long to look at your device, and they need to clearly see your intent. Where do you intend the gap to start from, and where does it end?

So yes, sharpies and stickers are both fine. If what you have is a back-board that you've written on, and then changed your design and written on it again, make sure you cover up the old writing.

Otherwise it's not clear...