SEO Q’s. Nofollow, dofollow, 301, etc.

After tinkering with my site for quite some time I’ve gone ‘live’ the first week of january. Steadily adding content and tinkering with the layout by using plugins and doing minor adjustments to my theme mostly.

I am however also in the progress of SEO-ing it.

I’ve already added better permalinks and good description and keyword tags.

But I’m wondering about ‘rel=’nofollow” – I’m currently using the ‘dofollow’ plugin, which says it disables ALL nofollows. Which is really not that great for SEO at all.

[Now the real question I want to ask is:

-How does wordpress -without any plugins- deal with nofollow?
-How do I get all links to be nofollow automatically unless I state otherwise?]

For example: I use some affiliate deeplinks, mostly below reviews. I want them to be nofollow. I also link between my articles, I want those to be followed.

Or is it just best at this moment to use no plugin and keep nofollow on automatically? (if that is what WordPress does)