The FTP password goes to the SyncNow vault: the PC keeps an encrypted copy only until the vault confirms it, and agents never receive it.
The Rules tab starts empty, with its own two tabs, Staging and Production: write there, with Add rule, what agents must always do or never do on the site, for example Never edit the files in vendor/. Rules need no approval and apply as soon as they are saved: see What is the Rules tab, and why should I write rules?. Since version 13.2.49.74 SyncNow no longer looks at the site by itself to propose facts about its web server, PHP version or framework.
The project also appears on your other PCs signed in to the same account, and while the app is open SyncNow checks the FTP connection in the background with a check that only reads. Then write down in Planning where the project is going and connect your agent: see What does my AI agent need to connect to SyncNow?.