Maybe this topic is better placed in "Tutorials". If yes, some admin may move there.
In XP (nativeEx and LiveXP) ice-age, app scripts got hard coded whether they should run directly from CD, or be included in the (provided by the nativeEx functionality) RAM disk.
Starting with Vista, NightMan invented the choice "Run from RAM", "Run from CD".
The app has been either included in the generated WIM, or copied to the "Rest of the world" in the generated ISO.
This method is used by most currently existing PE2 / PE3 projects.
With PE3 projects, the option to generate multiboot CDs, came up.
Here the first issue: (Example for the next is Opera-CD by Medevil, which can be run strictly from CD)
You generate a multiboot CD with PE1, PE2, PE3. All of the projects have Opera-CD. So it is burned three times with 6 MB to the final CD.
To avoid this redundancy, the option "Boot from BootMedia" is the solution. When creating the final multiBoot ISO, Opera-CD is only copied once to the root of the CD, outside the different PEx images. Shortcuts are adjusted to this configuration.
Now a small challenge:
You have an app which usually could run "Boot from CD" or "Boot from BootMedia".
But unfortunatelly this app sometimes updates some data from internet and writes them into the running PE, and therefore the data must be writable. Example: A virus scanner needs the latest data.
First solution: "Run from RAM" is not the best one:
When you are working with an old PC with maybe only 512 MB of RAM, RAM size could be insufficient to store the data. And next boot, you have to download the latest definitions again, ...
Better solution: "Run from VHD" (Virtual Hard Disk). The Virtual Hard Disk is an image placed "anywhere" and a writable file. All the new virus definitions are written into this file and available next boot.
FAQ: Where can I find all this functionality?
Answer: In multiPE