What you update and how it works depends on what you use.
Most automatic update scripts incorperate an index page and just choose the latest file which is released. Then run backwards, get the second latest and first to make the appropriate links.
You can get stuff like
iStrip with snaazy web interfaces and automatic record keeping. IStrip has a web form that lets you upload a file, add corresponding news and a title, and a release date.
When choosing what you use, you have to think about the bells and whistles and such. Do you need the web interface, or can you use something smaller and simpler which requires manually changing a file or database? Do you want it to organize your comics by date (which is rather archaic on the web) or by number? The less automated and detailed the script is, the easier it'll likely be to design your webpage.
I'm not quite sure what you meant by using comic.php on the front page. If you meant use whatever update/archive script as your home page you could name it index.php
If you're still searching for scripts, there's an old (circa 2004) list on
buzzComixHope that helps
