Well I have only had my Pineapple a day so far so I am a real newbie.
But I would consider this:
Ethernet into the Pineapple from laptop
Use a mobile device as a wifi hot spot or USB tether to laptop
use wlan1 for deauth attack
use wlan0 for Karma
I haven't looked into the Jammer settings but I think you can send a deauth to a specific SSID in CLI
probably rambling now but I would:
Eth Pineapple - Laptop
USB Driod - Laptop
connection share these 2
Wlan0 for Karma
and use my Laptop Wifi to run aireplay-ng -0 10 -a {BSSID} wlan0
I haven't tried this as I said I am just starting out really hope this helps.