I need to create one .pak file with program files (directories with files and so on) and then I'll need to update that .pak file but I don't know how to deal with .pak files since I cannot find any tutorial to them.
Handling those .pak files seems a little bit complicated to me.

Unpack this file inside your Esenthel\Projects directory:

  Pak Tutorials from EE1.rar (Size: 5.97 KB / Downloads: 20)

It contains a project with a sample pak file and 3 tutorials showing how to handle pak files.

You can also 'import' pak files (and also any other file types) in EE 2.0 via Raw files. In the project elements window right click and choose 'New Raw File', then right click on the newly created file and choose 'Reload' and point to your file. In code you can use EncodeFilename(*drag&drop raw file here*) in places where you need to use a Str filename, like Paks.add()...

Thanks for help!