Can I work at home and bring my site into college/the office/somewhere else? Yes, but you MUST keep all your imported media - graphics, sounds, QuickTime or Flash movies, etc. - with your Freeway document. Your layout doesn't contain your original media, it references the files. So if you open your Freeway document away from your other files it won't be able to find them. You have a safetynet of sorts for graphics, as there's an on-page preview that is stored on your document. But rich media isn't cached at all. Do not forget to keep those with your Freeway site!
Make your site using the Template approach so you get a ready-made folder structure, and use the Media folder this gives you to keep your various original media files organised and at hand. If you don't do this then at some point you will end up with missing files, and that point might be as you hand final work in for assessment or try to deliver final changes to a client!
Can I edit the HTML files that Freeway has made? Yes, these are standard text-based HTML files. BUT the next time you preview or publish from Freeway it will overwrite whatever you've done to those files in the designated 'Site Folder'. By all means poke around, reuse and tweak if you want to, but remember that this isn't the normal workflow process and it is therefore a trifle hazardous - in terms of losing your custom edits. If you want to add custom markup code this should be done within Freeway using its various features for extending tags or slotting in sections of code markup.
Why is my desktop suddenly full of HTML files? You have set your Freeway document to publish the files that make up your web site straight to the desktop rather than into a dedicated 'site folder'. This can happen if you create your site using the Custom option rather than the Template option in the New Site dialog. The first time you preview or publish, Freeway will ask you where to put the files it is about to make. Whatever place you pick is then set as the Site Folder for that document. You can choose File > Document Setup and set this to a folder you make just for this purpose. Once this is done just clear up the junk from your desktop; it is not needed any more.
To avoid this in future ALWAYS begin a new site using the blank template. This takes care of a number of details for you, including setting up a dedicated folder for the HTML files etc. that are produced from your Freeway document.