FileMaker Pro can host up to 9 simultaneous connections from FileMaker Pro clients. Each such user has to have a correctly licensed copy of FileMaker Pro or an iPhone or iPad with the free FM Go application in order to access the database.
FileMaker server will support many more clients and also provides a number of valuable tools for better managing your database.
For the rest of your questions, I suggest breaking them up into simpler tasks and asking them in the FM Pro Forum (see tab at top of this screen). You'll also be better able to ask questions and understand the answers offered if you invest in some training resources on FileMaker and relational database design.
In general, you would not give each site their own set of tables. Tables that combine data of the same type from all sources is a much more flexible way to go. A field in such a table can identify the site and you can even set up access controls that limit what records a given user can see in that table. But defining a good data model--the needed fields, records, tables, table occurrences and relationships is a crucial part of setting up a good database system and it is not a simple concept to take on. Be prepared for a cycle of trial and adjustment/redesign as you work out what is best to meet the needs of your particular system.
Please note that it is also possible to publish a FileMaker Database to the web and then your client users can use a web browser to access the database and enter data into the system.