I am new to automator […] I'm too much of a layman to know where to begin.
It's customary to begin at the beginning.
Mac 101: Automator
I'm not an Automator expert, so don't take my word for it, but I believe that what you need cannot be done in Automator; I don't see how the variable you need can be passed from one action to another.
It's been many years since my doing any scripting in FileMaker, so I don't know what it can do now and I don't remember much about what it could do back then, but I'd look first into ScriptMaker to see if it can't handle the whole job. If not, the solution is AppleScript. Don't bother with exporting—pass the file paths from the found set on to AppleScript as a list, then pass the list on to the FTP client. Use a client which supports AppleScript (eg, Fetch), or use the built-in ftp client with AppleScript's "do shell script" command.