Concept of Templates

Hello everyone, I have a simple question, and I hope I ask it correctly without any confusion. I want to build my own template scheme without using any 3rd party, ready-made freeware template codes. But I am confused about one thing. I am building a content driven website. The templates (such as html headers, footers, style sheets, etc) will be placed in text files and called in as includes, but the content will be placed in a database. The thing I'm confused about is the concept behind linking these articles together in a main TOC (table of contents) page. When one clicks on a topic from a main TOC page, how does the server know which article to pull from the database and place into a particular template? Does the link itself send any information someplace that tells the server what information is needed and how it has to be performed or placed? I hope this doesn't sound too confusing. If anyone needs me to clear it up a bit more, please let me know and I'll try my best. For those of you who know what I'm talking about, what is the concept behind templates, especially the links to those templates? Thanks in advance...