I have already began developing in PHP, but I have had various difficulties with the atmosphere: mysql server will not start, can't debug PHP code (despite determining PHP executables), installed apache2 also it did not work, installed Light but still nothing, etc.

Overall, it is simply been chaos, and so i made the decision to begin again(or other fix that may appear). Nevertheless, how do i setup a near-perfect PHP atmosphere in Eclipse by which I'm able to debug, run and merely not have access to all of this hassle?

I am running Eclipse Indigo with PDT and PHP 5.3.

Well...you can begin reading through this:

How To Setup a Local PHP Development Environment in Linux Ubuntu 11.04 with Eclipse Indigo 3.7, LAMP & Xdebug

Additionally I recommend setting up:

Eclipse Web Tools Platform (WTP) for the HTML/CSS development

Eclipse Data Tools Platform for the DB development. You may also use PhpMyAdmin.