This may not be entirely accurate but the information below is how the two list appear to work from what I can determine.
Whitelist:
The whitelist appears to be a list of SSIDs in which you want to the pineapple to mimic.
Example: There are 3 SSIDs announced nearby, WIFI_1, WIFI_2, WIFI_3. You add WIFI_1 to your Karma whitelist since you only want the pineapple to mimic the SSID WIFI_1. Any SSIDs not on the whitelist will be ignored, the Pineapple will not mimic those SSIDs.
Blacklist:
I believe this is a list of clients you do not want to connect to the Pineapple. For example, you want to add your own device(s) to blacklist to prevent your own WIFI device(s) from auto connecting to the Pineapple when it's deployed.
Hope that helps