Chromeless and swf's

[Ryukuchan]

This is a javascriptish/flash question.
I downloaded ByKlein Chromeless Windows 2.0 beta because the older version of chromeless was not compatible with IEsp1.
I want to simply put the flash file "index.swf" inside the chromeless page so it fits nice (Like in the older version) But I have found that it won't display flash files directly.
I know they work inside of html files. But I have so many flash files, as well as links to other flash files that would be a major pain. And I have set up my site to avoid using a ton of html files.
If I can directly link to an swf file am I going to have to fix all the links (which are inside the flash files) to other flash files? Cause right now they are just something like "bob.swf" which worked with the old version of chromeless and would just replace the current flash file with the linked one.
Help.