1. The easiest way to create a bootable flash drive is to use Rufus v1.2.0 Rufus - Create bootable USB drives
As in the screenshot select ISO Image in the dropdown menu, browse to and click on the bootable ISO and then click on Start.
2. You can store any data in the remaining space available and that will not destroy the bootability. But make sure you put them in identifiable folders. Otherwise it will mix with the files and folders of the extracted ISO. You delete any extracted ISO file/folder by mistake, that program will not run properly.
My personal advice would be to have a dedicated pendrive for your bootable ISO. If you have many bootable ISOs then use YUMI - Multiboot USB creator. YUMI - Multiboot USB Creator (Windows) | USB Pen Drive Linux
3. Your purpose will be served if you use EasyBCD (free for non-commercial use) EasyBCD - Take control of your boot loader | NeoSmart Technologies
and configure it to boot from the bootable ISOs stored in your internal drive. When the system boots you will be presented with a boot menu and you can choose to boot Windows (default) or any of the bootable ISOs run from the memory.
EDIT: Yep, I found this thread which I had read long back as a guest. Say "No" to burning bootable CDs, DVDs from ISOs
That should give you an overall idea.