It can often happen that the structure of a site - especially one with many QuickTime movies, large audio files or makes heavy use of multimedia content - will make Freeway upload the entire site even if a single file or page is edited.
A possible solution is to use a single resources folder for your document. Go to File>Document Setup, click on the Output tab and make sure that the Resources popup is set to "Common Resource Folder".
If that doesn't solve it, it might be that there isn't an easy fix in Freeway. There is, however, a reliable method to prevent this happening - it may take a few minutes to set up, but it can save a lot of time in the long term as the entire site will not need to be uploaded each time.
First, you'll need to download the excellent (and free) FTP application called Cyberduck from http://cyberduck.ch. Once you've installed Cyberduck you can then open your Freeway file and publish your files into a folder which can be set as a "watched" folder by Cyberduck. To do this, go to File>Upload, but this time choose "File Copy" from the Upload popup. Click on the Select button in the File Copy dialog, choose a location, create a new folder, give it a logical name, click Choose and then click OK to start the publishing process into the "watched" folder.
Next, launch Cyberduck, click on "Open Connection" then enter the Server, User Name and Password information (the same info you entered into Freeway's upload dialog when previously uploading direct from Freeway) into the relevant fields. Unless you place your files on the root level of the server, you will now need to open the directory (folder) on the server where you files need to be uploaded to.
With the site file directory open in Cyberduck, open your "watched" folder (where you published your files with the File Copy function), select all the files in the folder then drag and drop them into Cyberduck's main upload window. This will start the uploading process - but hopefully this will be the last time the entire site will need to be uploaded unless you make major edits to the site.
Once the upload is complete, you may want to set a bookmark for your web site folder on the server. Next, in Cyberduck, go to File>Synchronize, navigate to your "watched" folder and click Choose to close the dialog window. This now means that Cyberduck will compare which files need to be uploaded from the "watched" folder to the server and which ones don't.
Next time you make an edit to your site, use the File Copy method to publish the files into your "watched" folder again, launch Cyberduck, use the bookmark to connect to your server, go to File>Synchronize and choose the "watched" folder (it should be remembered) to start the uploading of just the files which have changed since the last upload.
We appreciate that this means there is an extra stage for each upload. We are working on a solution within Freeway which we hope will appear in a future version (but we can't be specific as to which version in which it might appear).