You should go with one theme. Parts of the site that are controlled by the theme remain static, no matter what content you're working on whether it's a page or blog post. Those things include the header and footer. I don't see how you could have multiple conflicting versions of those files in a single installation. Those files are important to SEO.
If I were you, I'd customize the existing theme(s) to include the features/functions you're currently lacking rather than try to integrate two different themes and multiple plugins (never mind the additional maintenance Unikey mentioned). I'm assuming you're using an SEO plugin but even if that's not the case, you probably have others that you will want to continue to work seamlessly.
Someone else might have experience with this. I don't, meaning I've never tried to optimize a site that uses two simultaneously installed themes. Hopefully they'll chime in if they have a different opinion. I'll be interested to hear.