Good question, sorry I didn't explain that more. There are two ways to put the Epsilon into boot mode.
The first is to use the hardwired reset switch. Hopefully you will never have to do that. On the board itself there is a ISP footprint under the spacebar that has some extra text that says "RESET". If you short those two pads while it is plugged it, it will reset in BOOT mode. With the open case design, it is possible to reach those pads without removing anything. I use a pin or paperclip.
The second (far more useful) method is to use the SCANCODE_BOOT assignment. I suggest you always add this to your Fn layer. The boards I sent out should have this mapped to Fn+Esc. It will immediately reset and jump to the boot loader.