Most linux ISO files will just work if you just copy them to an E2B 2nd level folder such as \_ISO\MAINMENU, \_ISO\AUTO or \_ISO\LINUX.
Note: linux .iso files can be renamed so that they will be listed in the menu as whatever you wish, e.g. \_ISO\LINUX\ubuntu 16.04 (64-bit).iso64 will appear as 'Ubuntu 16.04 (64-bit)' in the Linux menu (set EXTOFF=1 in \_ISO\MyE2B.cfg file so that the .iso file extension is not listed) or another example: \_ISO\LINUX\Mint 18 Cinnamon (32-bit).isodefault.
If you want to add help text below the menu, use the TXT_MAKER.exe utility to make a .txt file.
E2B automatically makes a new Type 0 partition table entry on the E2B drive (partition #4) when you select an ISO file from the E2B menu. Most linux LiveCD ISOs will automatically mount this Type 0 partition and so it will be able to access all the files inside the ISO during 2nd stage booting. In this way no special, version-specific, 'cheat codes' are required and the linux distribution does not need to be identified by E2B. 99% of linux LiveCD ISOs just work!
Because we are booting directly from the original ISO, we will also see the same boot menu choices that you get when you boot from the original CD. With other utilities such as YUMI or XBOOT, you often do not get the same boot menu because they use their own boot menu.
Always check the List of test ISOs for your particular linux distribution, to see if any 'special' tweaks are needed.
Tip: If booting via 'ISOBOOT' or persistence ext files, ensure there are no spaces in their filenames.
You can also check my blog for posts about E2B and linux.
Installing linux from an ISO
If you boot a linux install ISO which can install linux onto another drive, you may find that it cannot find the 'CD' and ask you to install a driver. In this case, select 'cdrom' device from the menu and then change the device path from /dev/cdrom to /dev/sdX4 (where X is the USB drive - e.g. b or c or d or e).
Alternatively, you can convert the ISO file to a FAT32 .imgPTN file using MakePartImage.
Some Linux ISO files can be run with persistence. In this case, each ISO will require a special .mnu file. Look in the \_ISO\docs\Sample mnu Files folder for a range of .mnu files. Typically, you will need to create another file formatted as ext2 using RMPrepUSB which will be used for persistence. Do not use spaces in the persistence filename.
Install multiple linux OS's
Provided that a linux distro will install to a single ext2/3/4 partition, it is possible to have multiple, fully-installed, copies of many different linux OS's on a single-partition E2B FAT32 or NTFS USB drive. Each OS is self-contained and fully installed just the same as if it was installed on an internal hard disk (i.e. not 'LiveCD'+persistence, but a full linux OS install). For details on how to do this, read this blog post.
Before running E2B, use the \MAKE_THIS_DRIVE_CONTIGUOUS.cmd script or Ctrl+F2 in RMPrepUSB to make all files on the E2B USB drive contiguous.
In linux, you can use defragfs to make a FAT32 E2B drive contiguous or udefrag for NTFS drives (see \_ISO\docs\linux_utils folder).
If the \_ISO\CONTIG.ISO file is present and if it is large enough, if the linux ISO is not contiguous, E2B will copy it to the CONTIG.ISO file first, to make it contiguous (CONTIG.ISO should already be contiguous).
If CONTIG.ISO is not large enough for your ISO (i.e. your ISO is larger than 500MB), simply delete CONTIG.ISO and copy any larger file to the E2B drive and rename it as \_ISO\CONTIG.ISO. Then make it contiguous using defragfs or udefrag.
If the ISO cannot be made contiguous, E2B will automatically attempt to use ISOBOOT.g4b. This is a grub4dos batch file which attempts to identify the ISO from it's filename and then uses special 'cheat codes' to tell linux where to find the ISO file during 2nd stage booting. The method is similar to the methods used by many other multibooters such as YUMI, XBOOT, pendrivelinux, etc. As such, it may not work for all distributions and versions of linux. ISOBOOT.g4b may need to be constantly updated whenever a new distro is arbitrarily changed by the developers!
Note: The linux filename should not contain any spaces. Use underscores or hyphens instead.
You can force E2B to only use ISOBOOT (instead of using it's usual method of booting an ISO) by holding down the SHIFT key before selecting the ISO menu entry and then pressing [Enter].
If your linux ISO supports UEFI booting, you can use MakePartImage to make a FAT32 partition image (.imgPTN) file. This will allow you to MBR or UEFI boot.
Booting from a partition image (.imgPTN) file with persistence is not supported using .mnu files, however it is possible to modify some versions of linux (e.g. Ubuntu) to support UEFI-booting with persistence.
Grub2 menu system
If you install the E2B grub2 menu system, it is possible to UEFI-boot directly from many linux ISOs (even those that don't officially support UEFI-booting!