Either — they're built to work both ways.
Barefoot is where you'll notice the footbed most: it has a soft, suede-like top layer and subtle toe ridges that your toes press into as you walk. With socks that texture is less pronounced, but nothing about the fit or support changes — the Flyknit upper stretches to accommodate either.
Most people end up doing both: barefoot around the house in warmer months, thick socks in winter.
One sizing note: if you're between sizes and plan to wear them with thicker socks, size up.
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