There are several ways to achieve this.
You may now or later want some pages to have a standard or default swf
A simple but reasonably versatile method would be to :
Create a TV [*FlashHeader*]
Give it a default value of {{CustomFlash}}
Place [*FlashHeader*] in your template
Assign it to your template
Create a chunk {{CustomFlash}}
For the content use your embed/object code as normal but replace the swf file name with [*alias*]
e.g.
<param name="movie" value="assets/templates/default/images/[*alias*].swf" />
Create another chunk {{DefaultFlash}}
For the content use your embed/object code as normal referring to a default swf file
Tested with images, but not flash!
David