Can you provide the following env variables?:
$ALTERAOCLSDKROOT
$AOCL_BOARD_PACKAGE_ROOT
$QUARTUS_ROOT
It looks to me that your Bittware BSP isn't installed in the correct location. Bittware should have documentation on how to install it in the proper locations. I believe it came with the BSP. Modify the items below based on the location of your Quartus installation
1. $ALTERAOCLSDKROOT should be /root/altera/hld
2. $AOCL_BOARD_PACKAGE_ROOT = $ALTERAOCLSDKROOT/board/apbpp_v14.0 (although I would change it to bittware or something more meaningful )
And as RT137 said, run aocl install as root.
You will have to set $QUARTUS_ROOT and $LM_LICENSE_FILE correctly.
As far as flashing the board, see the following thread. Bittware had an error in their documentation. Not sure if it has been addressed.
http://www.alteraforum.com/forum/showthread.php?t=45702 Let me know if this helps,
Rudy