The color property works as long as you're using things supported by regular CSS. For gradients you'll need the replace call.
As for which files you are supposed to use, I don't know. You have the freedom to use any file you like. Therefore, you should probably get more familiar with Joomla and find out where the "correct" files are.
Also note that the code you posted is just an example, your own files may differ.
Simo
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Usually, yes. There are sometimes exceptions, one of which I mentioned in the previous message.
You always have to have a replace call, otherwise Cufón doesn't know what to replace. If you are having a hard time integrating this into Joomla, perhaps following our documentation and constructing a basic example first would make it easier.
There may also be a plugin for Joomla, although if there is it will be a 3rd party one and therefore I cannot give any guarantees about functionality or ease of use.
Simo
JavaScript code does not go into CSS files :)
Simo