For javascript files when you say activate I presume you mean to make the bundle active in the Bundle Editor. You also need to select the Prototype and Scriptaculous bundle in the bottom of the editor window, it'll remember the selection for .js files after that.
As for HTML files... that won't work. There's currently no way to extend a bundle, you can only replace it. HTML includes the javascript bundle, there no way for the Prototype bundle to be called into the process.
Ah, ok. Did not get the last part. THat's ok though, since it encourages separation of files and such stuff. Thanks a bundle ;)
Andreas