How to manage slugs with Custom Post Type and Taxonomies?

I’m using Custom Post Type for my portfolio items, and a custom Taxonomy for the portfolio categories. But I can’t figure out how to manage the slugs, in relation to my blog post slugs. This is what I want to achieve.

Blog post slugs
For my blog posts, for example I’d like to have categories thoughts, updates, and articles. With slugs like this:

• domain.nl/blog/thoughts/title-of-blog-post-1
• domain.nl/blog/thoughts/title-of-blog-post-2
• domain.nl/blog/updates/title-of-blog-post-3
• domain.nl/blog/updates/title-of-blog-post-4
• domain.nl/blog/article/title-of-blog-post-5
• domain.nl/blog/thoughts/title-of-blog-post-6
• etc

Portfolio post slugs

For my portfolio items (projects), for example I’d like to have categories websites, graphics, and presentations. With slugs like this:

• domain.nl/portfolio/websites/title-of-project-1
• domain.nl/portfolio/websites/title-of-project-2
• domain.nl/portfolio/graphics/title-of-project-3
• domain.nl/portfolio/presentations/title-of-project-4
• domain.nl/portfolio/websites/title-of-project-5
• domain.nl/portfolio/presentations/title-of-project-6
• etc

My questions

What I’m struggling with are things like this:

• How should I set the general permalinks?
• How should I organize and set blog post categories?
• How should I organize and set custom post type for portfolio items (including slugs)?
• How should I organize and set an extra, custom taxonomy for portfolio items (including slugs)?
• Are there other things I should consider?
• When do I need to save permalinks an extra time?
• etc

Is there a clear tutorial about this? Really getting confused, don’t know how to get it done…