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FreeNet is a distributed key/value store. It can be used to store files by storing the contents of the file under a key that is the hash of the file content. Generally you operate on Freenet at the level of keys and values.

ZeroNet operates at the level of sites. Sites contain multiple files. Seeding of data happens at the site level.

You could implement ZeroNet on top of Freenet but implementing Freenet on top of ZeroNet wouldn't make much sense.

When inserting new data, Freenet pushes data out to nodes. ZeroNet pulls data from requestors. With Zeronet you can't disconnect your node until other nodes have a complete copy if you want the data to remain available. It is difficult to tell when it is safe to do this. With Freenet the data isn't stored on your own node, it is pushed out to other nodes when first inserting. When the insert completes you know you can safely turn off your node. The data remains available.