Please help! CCK/taxonomy for multiple linkable categories

I am new to Drupal, and though I've read a couple of books now and did multiple tutorials, I can't find an answer to my problem.

Basically, I am putting together a site that catalogues certain archaelogical information. The main information comes in two parts -- Article about a site/structure and images. So I'm creating two content types (article/image)

My question is:

For the article, how do I create multiple categories so that when people click on them they could see all results with that category. Eg: Location ... Africa, Egypt... So that people can click Egypt and all egypt articles pop up, click Africa -- all Africa (including Egypt) articles pop up. Then there is Type, Size, Historical period, etc... Each category has to be a link to all other articles in this category.

I've tried Taxonomy, and created multiple vocabularies -- but all the words appeared at the bottom of the article in one long line, and I need them sorted by categories. I tried creating fields with CCK, but then terms appear as plain text, and not linking.

What modules do I need? What am I missing?

And also, I understand that I can link the image content to the article about it via node-reference in CCK. But how can I display the images next to the article itself? Is it something I have to use Views for? Or do I somehow insert a field in article to reference all images that have a matching title?

(I have to keep images as a separate content type because there is a set of image specific information that has to be stored, such as description, source, tags, etc...)

Sorry if this is a silly question, but I really can't find an answer and I've been trying to solve this all week...