Can I Start Hostapd-Wpe Over SSL without loosing the connection?

I am running kali linux on a raspberry pi 3 with an wireless adapter. I have no problem running hostapd-wpe local but to be mobile i want to control my RRI over ssl. Connecting a hotspot from my phone to the build in wireless card of the RPI. The problem is that i have to run airmon-ng check kill to kill the processes that interfere with hostapd-wpe which are sadly also essential to keep up my ssl connection. I am using my wireless adapter for hostapd-wpe so can i somehow only kill the processes on that adapter keeping them running for the build in wifi card??? Or do i have to find a other way to remote control the RPI? A other idea would be to write a script that executes the two commands (airmon-ng check kill and hostapd-wpe /etc/hostapd-wpe/hostapd-wpe.conf) upon start-up, hosted-wpe dose save its results so i could access them later... but would not be abel to change anything on the road... would this be a good solution and how would the script look?

I am pretty new at this so all help is greatly appreciated

Thanks