Ssh to aTV then type in these commands:
sudo su
root/alpine
cd /Library/LaunchDaemons
launchctl unload com.plex.plexconnect.bash.plist
Ssh to aTV then type in these commands:
sudo su
cd /Library/LaunchDaemons
launchctl unload com.plex.plexconnect.bash.plist
Done! Now how should I launch plexconnect manually and the CTRL + C to kill it. Not sure but the command should be "launchctl load com.plex.plexconnect.bash.plist" ?
You basically just did when you unloaded it. You can load it back up by rebooting your aTV or Ssh back into the aTV then type in these commands:
sudo su
cd /Library/LaunchDaemons
launchctl load com.plex.plexconnect.bash.plist
Whats the best way for me to connect to my ATV3 over a wan?
Have a local PlexConnect "server" with your aTV and use myPlex...
When I travel with a aTV 3 I use a old jailbroken iOS device as a PlexConnect host then like baa said I sign into Myplex to access my content from home since he implemented that feature. Here is a link you can try if you have a old or new device jailbroken you want to try to use:
https://forums.plex.tv/topic/88975-plexconnect-running-on-any-jailbroken-ios-device/
I have a plexconnect setup over wan and the open dns port is a very serious issue. Port 53 gets scanned about every 5 minutes.
i use a whitelist to protect the open ports. Basically your ip (dyndns) needs to be on a list for the firewall to let you connect. Works nicely from everywhere…

Lucian,
I presume you put in your WAN IP (of the Plex Server site) in the ATV (on the remote site) at the dns setting?
The issue (I would have) with that is that my WAN IP changes every now and then. And you can't put in a (dynamic) host name in the ATV.
Now my parents have a local PlexConnect running, with that there's no issue as they use myplex and the plex server automatically publishes himself on the right WAN IP...