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.

This is definitely one of those things where you can talk to 10 different people and get 5 different opinions.

The best detailed resource that I've seen on this was written by Dan Shure. I highly recommend you check out his entire post on the subject: http://www.seomoz.org/blog/setup-wordpress-for-seo-success

He details step-by-step how he handles each, and gives the reasoning behind his choice.