To program the BLEPad, connect it to the computer with a Micro-USB cable. Select "LilyPad Arduino USB" from the Tools > Board menu.
Differences from Other LilyPad Arduino Boards
The BLEPad uses a single processor (the ATmega32U4) to both run your sketches and communicate over USB with the computer. This provides more flexibility - for example, the board can emulate a keyboard or mouse - but it also means that the USB connection resets whenever the processor does (e.g. when you upload a new sketch).
Uploading Sketches to the BLEPad
Typically, you'll upload to the BLEPad as you do with other Arduino boards: select "LilyPad Arduino USB" from the Tools > Board menu and the appropriate serial port from the Tools > Serial Port menu and press the upload button. This will reset the BLEPad, launching the bootloader, which receives the new sketch from the computer and stores it on the board. The bootloader then automatically launches the new sketch.
Sometimes, however, this automatic reset fails. This can happen, for example, if you upload a sketch to the BLEPad with a different board (e.g. the Leonardo or Micro) selected in the Tools menu. If this does happen, there's an easy fix: you can press the reset button on the BLEPad twice in quick succession to initiate the bootloader. To upload with this technique, first press the upload button in the Arduino software; then, when you see the status message "Uploading..." press the reset button twice. This should initiate the bootloader, and the Arduino software will upload your sketch. You might have to play a bit with the relative timing of pressing the upload button in the software vs. the double-press of the reset button on the board.