How do logia users fly with their ability/element? I thought they are only able to turn into their element, not control them.
Logia users, whose element is lighter than air, can fly by transforming (at least) their lower body into that element: Moku Moku no Mi (Smoke fruit) Gasu Gasu no Mi (Gas fruit)
I am unsure if the Pika Pika no Mi (Light fruit) is based on the same or rather the special property of light.
I am not aware of other Logia users truly flying with their ability. They rather propel themselves into the air (e.g. Mera Mera no Mi / Fire fruit and Suna Suna no Mi / Sand fruit).
The Yuki Yuki no Mi (Snow fruit) can grant flight by creating wings made of snow but that is less of a Logia thing itself.