Where to start?
The_GUI is kind of application that needs some knowledge in order of get the most of the offered posibilities.
The_GUI don't pretend to be simple-to-use CD recording application. The_GUI's accent is on making bootable cds. Yes, you can do that with other applications, but the posibilities offered by mkisofs are unique, and they are not offered in any other application. The_GUI tries to bring those posibilities to you in the user-friendly manner.

Where to start?

Let's begin through an example.
First, make a folder that will be the root of your new CD. Use your favorite file manager for that. Now, put all the files you want to burn in that folder. If you are making bootable cd, then you have to follow folder structure rules for the kind of CD you are making, e.g. if you are making Isolinux bootable CD, you need to make folder named ISOLINUX and to put in isolinux.bin and isolinux.cfg files, etc... I don't want to go further with explanation on that, consult your bootloader's manual on folder structures and rules.
Now, start The_GUI and let's do something useful with it.
First, for some bootloaders you need to remove read-only attributes on some files, use "case and attributes" module for that.
If you are making WinPE (BartsPE) CDs, and you don't wan't to use original ISO-making tools, you may need to change file/folder names for some files/folders to uppercase. For this you can also use "case and attributes" module.
Next step would be optimization of files order on CD. If you are involved in making PE cds (WinPE, BartsPE), you have noticed long boot times. This can be optimized by telling to mkisofs.exe in which order to put the files in ISO file. If you know in which order the files are loaded from CD on boot, you can optimize the boot process by using "Layout sorter" module and SORT option in "Make ISO" module.
Next step in building your bootable cd would be making the ISO file. Use "Make ISO" module for that. This module is full with various options about filesystems you can use, infos that can be saved on CD, etc...
Explaining each option would take me my whole lifetime (because I'm bad in explaining, and specialy bad with English language). Please consult mkisofs documents included in this helpfile about mkisofs options. If that wasn't real help, please take a look at links section, you can find a couple of useful links there.
After building ISO file, you can burn it to the CD by using "CD operations" module. In this module you can also find a couple of other helpful functions. I hope I don't nees to explain them.
Last module is "Other". Here you can do some operations about boot sectors and boot images. You surely know that bootable cds are containing boot loaders or boot images (images of ordinary floppys). Here you can extract boot sectors, make images from floppys, write those images back to floppys, etc.

The_GUI modes:

Click on The_GUI icon to start program in normal mode. In normal mode no temporary files are used, so this mode can be used to start The_GUI from read-only media or from r/w media if no log files are needed.
There are also a couple of command line switches:
-win98   -- run The_GUI in Win9x compatibility mode. Temp files are used because Win9x cann't handle more than 64kb buffers for some components. For this mode The_GUI needs to be started from r/w media.
-debug  -- run The_GUI in debug mode. Same as checking "Debug this session" on the program's first screen.
-win98debug  -- run The_GUI in debug mode with Win9x compatibility. For this mode The_GUI needs to be started from r/w media.