It's a little confusing. You would only use the app on a new device to assist in transferring from another Samsung afaik..
The Smart Switch pc program is independent. If you can still use Kies for the S4 and S3, Kies allows syncing of Contacts, Photos etc.
Most times now if you tried to download Samsung Kies fresh you would be prompted to use the newer Samsung Smart Switch program instead, as it seems they are trying to phase Kies out.
Smart Switch will also do backups and provide drivers and has a few other features but doesn't sync or copy files you can access, IIRC.
If you both drag and drop files or save to cloud storage or your online Samsung account, (most people don't sync to Kies anyway), I would use the Smart Switch program if it is compatible with the S3.
I used it later on for my Note 3 until I sold it, so it should be fine for the S4.
This is only my recollection, so is not definitive. I remember being able to browse options in Smart Switch as to what is backed up.
Smart Switch, like Kies, won't make a complete backup of your phone so use the Samsung account and other options as well.
(I'm trying to write this on a bouncing bus and suddenly wish I had a Blackberry Priv physical keyboard, lol.
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