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Both come up with the same reading and definition in Jisho.org (round/circular), and both are listed as common words. Is there any preference between the two or should I simply learn both as interchangeable?
丸い generally refers to spherical objects like a globe.
円い generally refers to circular objects like a circle drawn on a page. Perhaps also a physical object which is flat and round in shape (a 円 (yen) coin for example)
円 is usually read えん, and reading it まる sounds like ateji, and is less common. 丸い should be used.