Meanwhile you use thin enough cables, yes you can put the battery and the cover again. you can take a look at http://en.qi-hardware.com/wiki/Serial_console#Hardware_mod_to_have_a_pluggable_serial_port to see how I done a plugable serial port.
The other two pads are also the same serial port but was not active in the last u-boot release, they will on next release of the bootloader and will avoid the current serial/keyboard interference mentioned on the video. But be aware than this pads are very close to each other so good soldering skills (or good luck at first try in my case :P) is required to avoid to bind them together