Installing PHP, Ffmpeg And Things On Debian GNU/Linux 4.0

I have a shared hosting account on dreamhost
It has php and others installed but it allows custom installations for a number of reasons (control of the php.ini file, ...).

I have shell and ftp access to /home/username/ where my websites are
(/home/username/domain.ltd)

I installed php 5.2.9 under /home/username/php5,
I also installed ffmpeg but I ran into troubles installing ffmpeg-php.

Now I would like to start over, I'm not very advanced in this and I probably messed some stuff up. It seemed like a good idea to ask for some general advice before going at it again.

First, I was wondering about the filesystem I needed to set up, like the bin, tmp, lib, ... directories. Which ones do I need and what should go in them.
And how exactly do I let the system know these folders are there and it should look there for some commands. When I used phpize, it used the default one instead of the one in my custom php folder. Is the export command all there is to it?

When I install PHP, where should I install it and do I need to point it to my directories (bin, lib, etc...) instead of the ones in the host's root.
I noticed when installing ffmpeg-php it still looked for the default ones at some points:

HTML Code:
"checking for PHP includes... -I/usr/local/include/php -I/usr/local/include/php/main -I/usr/local/include/php/TSRM -I/usr/local/include/php/Zend..."
I don't know if this is normal behaviour or not, I'm just basically writing everything I am unsure about.

I got my website to use the custom PHP by editting the htaccess file

Also,
what would be the best approach to remove the things I currently installed, I suppose remove the php5 directory is not enough.