If I understood you well…
The Vanilla theme has two kind of tiddlers: themetweak/settings and CSS tiddler. Maybe you only need to change The part of CSS. Then you have to options:
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You could add a new CSS tiddler to the vanilla theme, it will use the Cascade of CSS to overwrite the previous styles (only you have to ensure that your new styles are loaded after of the originals). It is similar to how works the themes based on the vanilla theme (reusing the selectors).
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The hard way. You will need to know the structure of the layout and its selectors and then you have to create your styles, it you could reuse some selector o create new selectors. But you maybe have to solve problems of specifity in your styles.