So you moved your Database files to the server and now relative path references to external files don't work right?
A relative path tells filemaker "open 'filename' that is stored in the same folder as I am". The key here is that "I" refers to the database file, not your applicaton. Hence your references no longer work.
I can explain why they don't work. How to make them work in a server environment is more complicated. I think that if I were in your shoes, I'd install a copy of Filemaker Pro on your server, (don't run them both at the same time!), use it to open your file from it's new location, then relocate files/change their references paths until they work for you. Now quit FMP, host them on server and see if they work.
For importing from files stored on client machines, you may need to open a hosted copy of your hosted database and update your scripts and data references to find the files on your client machine without using a relative path. Whether this works for you will depend a lot on how you have set up each client machine and what you are trying to do with these external references.
Hope that helps.