Both separate CSS files for IE and browser-specific CSS in a common stylesheet have their adherents. I've used both methods for TikiWiki and its themes, but generally these days I like to keep the IE property variations close to the default (modern browser) ones because I find it easier than having to deal with the extra files. But this is a matter of personal style, for sure. To the best of my knowledge, though, the "hacks" I use, which are widely used and valid CSS, aren't nasty and fragile, as far as that's concerned.
Anyway, an easy way to use Tiki's css/ie6.css for your site would be to just add your selectors/properties to that file. This would apply to all themes since the file is called regardless of what theme is active.
I'm not sure about a smarty variable for path to style directory.
If you need special (and different) IE treatment for more than one theme, you could duplicate header.tpl and make a theme-specific version of it that contains the link to the theme-specific ie.css rather than (or in addition to) the default ie6.css.