PHPBB and other forum software use ID's to connect topics to posts
How do I add something like this in a custom script?

you have a field in the posts table that has the topic parent id

Your question is a bit vague too.

If you told us what you want your script to do, and showed us the script thus far, we could probably assist a bit more.

Cheers

I'm working on a helpdesk program and I want to be able to connect replies to the main question. Unforunately I don't know how to add IDs to the tables.

ALTER TABLE table_name
ADD id INT(10) auto_increment primary key

or better yet, download NAVICAT and do those in a friendly click tack enviroment