Hi,
Regarding your main site va your ftp site, it’s OK to have 2 managed certificates (one for your FTP site and one for the aimer-stock.com website). Your FTP site doesn’t even need to use a wildcard if the ftp site is always called ftp.aimer-stock.com, so you could set the domain for the certificate to be ftp.aimer-stick.com so you can tell the difference between the two certificates.
The “Single Site” choice targets the specific IIS site you have selected in the dropdown, which in this case is your FTP site.
Regarding Filezilla not being able to connect to your ftp site I’m afraid I don’t regularly use FTP or Filezilla so I can’t provide much advice on that but I do notice that “ftp.aimer-stock.com” does not resolve, so there is probably no DNS entry.