1] I used a minimal Debian 7.1.0 i386 in a VirtualBox VM for compiling script.bin. Also, I wrote the Emdebian image found in the following link to a SD card for the OLinuXino A10S: https://docs.google.com/file/d/0B-bAEPML8fwlZ2g0V0JSRGxHc0U/edit?usp=sharing. The script.bin file produced here was tested against Linux kernel 3.4.61. I believe it should also work for the kernel with the mentioned image.
2] Login as a regular user in the Debian VirtualBox VM.
3] Install OpenSSH client software if this will make file transfers convenient for you:
# su -c "apt-get install openssh-client"
4] In the Debian VirtualBox VM as a regular user:
# mkdir ~/olinuxino_a10s ; cd ~/olinuxino_a10s
5] Download fex2bin_bin_fex_tools.tar.gz in the ~/olinuxino_a10s directory you've created:
# wget http://www.malaya-digital.org/fex2bin_bin_fex_tools.tar.gz
6] Untar fex2bin_bin_fex_tools.tar.gz:
# tar xzpf fex2bin_bin_fex_tools.tar.gz
7] Copy the script_a10s_linux_HDMI/script_a10s_linux_HDMI.fex file from the first partition of the SD card having your Emdebian image to the directory ~/olinuxino_a10s you've created in a previous step. Or, you could wget it:
# wget http://www.malaya-digital.org/script_a10s_linux_HDMI.fex
8] Open script_a10s_linux_HDMI.fex in a text editor. Then look for the following:

rtc_used = 0
rtc_name = "pcf8563"
rtc_twi_id = 1
rtc_twi_addr = 81

Assign "1" to rtc_used, and "2" to rtc_twi_id:

rtc_used = 1
rtc_name = "pcf8563"
rtc_twi_id = 2
rtc_twi_addr = 81

9] Compile ~/olinuxino_a10s/script_a10s_linux_HDMI.fex to script.bin:
# ./fex2bin_bin_fex_tools/fexc script_a10s_linux_HDMI.fex script.bin
10] Overwrite the script.bin on the first partition of the SD card with the one you've just compiled in the previous step.
11] Insert the SD card into the OLinuXino.
12] Your OLinuXino A10S should now automatically save and retrieve the system time from MOD-RTC.