Hi Nathan,

Despite using a different plugin, I think Dan's advice still applies.

In general I suggest INDEXing the categories. Make these your keyword rich overarching categories.

For archives, I'll general NOINDEX those. They're likely not providing a lot of value to searchers, and could possibly create duplicate content.

For tag archives, I also suggest NOINDEX.

As long as you INDEX your categories, then you can kind of just follow your heart with the rest of them. Luckily, there really isn't a worst case scenario. If you're nervous, then just don't NOINDEX anything and see what happens. If you're happy with the SERPs then keep it as is.

I know it's awfully stressful to make sure you get this all correct at the start, but I promise this won't make or break your SEO. Feel free to experiment to see what works best for you.