That tutorial is not the best, but you can trial and error your way through it eventually.
This really isn't a guide, just my notes I use to make my own remaster.
https://docs.google.com/document/d/1SyfVq7e5nw9BqOhzQ8piB9jK43ieubkFFOOY-4DGuv8/editlet me know if I can assist with anything.
-------------------------------------------------------------------
Now to answer your question
when you start the program, you are presented with a GUI where you select the original .iso file you want to work with.
You create a new project, then open a chroot winndow
In this terminal window you can install and remove programs just like you would on your installed linux system.
So for examaple, if you wanted to remove libreoffice to save space, you would type "apt-get remove libreoffice-base"
And to install, lets say gpodder, you would type " apt-get install gpodder"
If you do nothing at all in the chroot terminal and make a new .iso from your project, it will be exactly the same as it was when you started.
When you are done making your changes, type "exit" to get out of the chroot terminal and finish your project.
If you want, try out my remaster. I'm always eager to see what people think about it.
https://www.dropbox.com/sh/y79exkhs2m1gnyw/7qqmibXwKB