You can remove the E2B Main Menu entries and just have the one menu if you wish.
This shows the default E2B menu with just one Clonezilla ISO file added to the \_ISO\MAINMENU folder.
If you do not want the DOS and UTLILITIES menu entries to appear, simple ensure that the \_ISO\DOS and \_ISO\UTILITIES folders are empty (or rename them).
If you want to remove the Windows Install menu entry, simply ensure there are no .ISO or .IMGPTN files under \_ISO\WINDOWS. You can suppress the Windows Install menu entry even if there are .ISO or .IMGPTN files under \_ISO\WINDOWS by using set NOWINMAIN=1 in your \_ISO\MyE2B.cfg file.
The Help, Boot to first HDD, Rebuild Main Menu, Reboot and Power Off menu entries (F1/F7/F8/F9/F10) can also be suppressed by using settings in the \_ISO\MyE2B.cfg file.
To use an existing template, copy the \_ISO\docs\Templates\MainMenu Only\MyE2B.cfg file to \_ISO folder on your E2B USB drive.
This shows the same E2B USB drive but with the 'MainMenu Only' MyE2B.cfg file added.
The 'Set default menu entry and timeout' Main menu entry can be suppressed by using set DEFMENU=0 in your \_ISO\MyE2B.cfg file.
Note: If you have no user payload files or .mnu files present and you use the MainMenu Only configuration file and use set DEFMENU=0, then because the menu will be empty, E2B will just boot to the grub4dos prompt. Please ensure that at least one payload file is present in the \_ISO\MAINMENU folder.
If you want to add Windows Install ISOs to the Main menu, please see this page.