I did not see anything written in the quick-start guide about migrating from a non-factory firmware such as TomatoUSB to LEDE. Is there any issue simply updating from TomatoUSB's Admin>Upgrade section? I am assuming one should check the "After flashing, erase all data in NVRAM memory" button from within Tomato.
Your current 3rd party firmware probably has some documention to revert back to the original vendor firmware, use that approach and then install LEDE from the OEM firmware.
While it might be possible to switch between different 3rd party firmware directly, doing so isn't tested and might fail badly, depending on the particular device and firmware (if said alternative firmware replaced the bootloader or changed the expected OEM mtd partitioning).