Each domain needs to have it's own directory and everything in a domain needs to be in that directory. The server needs to be set up to direct each domain to the proper directory for that domain. This is most easily done if there is a software control panel for the hosting account, otherwise there is a server config file that needs to be manually edited. Once this is done each domain will be able to be accessed with the domain name in the URL and each domain directory will be able to be accessed through FTP set up for each individual domain. From any one domain directory you will not be able to see of access any of the other domains.