you can open Flash5.0 files with Flash MX but not the other way around… the other thing is, if you want the file to be openable from Flash 5.0, but you’re creating it in MX, then you need to “Save As” Flash 5.0. Otherwise it will save it as an MX file.
Depends upon how big your site is. If it’s just 100k total, then I’d say use scenes and frame labels to make the whole thing in a single swf. If it’s any larger than that, then you should look into the loadMovie(); command.
What is done in that case is, each section is saved as it’s own swf. Then each swf is loaded into the player using action script. There are many posts on this subject here… if you need help locating them, let me know and I’ll find some links for you to look at.