zarklon wrote:If It works with Auto Emergency Jump mod then I'm gonna switch to this one. But I just cant get it to initiate any kind of way

Probably doesn't work, AutoTrader seems to replace vanilla scripts, and you could say that mods that replace vanilla scripts are by design made to be incompatible with mods that needs to add stuff to these scripts.
There actually are ways to avoid that incompatibility.
For example by calling AutoTrader scripts on top of the vanilla scripts. The thing is if he does that, he takes the risk of making AutoTrader incompatible with mods that bypasses vanilla scripts... So yeah. Also it would make uninstallation more complicated (and basically would have do what I do with AEJ, kill job ships and set player ships to "stop" or "follow").
The second option would be to add some code to AutoTrader's scripts. That code can be found here
http://forum.egosoft.com/viewtopic.php?t=371733 , under "compatibility". That code adds some "blocking actions" though.
Anyway, AEJ will still work even if nothing is done, but not for your auto traders / miners. NPC ships will be fine, all your combat ships too, station miners / traders too.