question about moving php code to a drupal module

I have a fairly large codebase that I'm thinking about moving to drupal. My current site does a lot of of index.php?query=something and was wondering how in Drupal I would handle this. I was able to create a custom module and output the information but how would I do something like create a search results page?

Also, I'm having a problem when I create a "page", I put some custom php code into the page. The problem is that this now shows up on all "pages". I'm not sure why this is working this way.

thanks,

jonathan