In a multisite setup, you need to adjust the upload_path for each individual site through the Network Admin menu.
Go to /wp-admin/network/sites.php. Edit the site in question. On the settings tab, you can find the Upload Path setting and change it to whatever you want.
You can also adjust the URLs on this page. Look for “upload”.
Note that this doesn’t apply retroactively. Only new uploads will be affected.
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