That's a bit weird indeed. It will be saved in SAM/aircraft.xml. From there you need to copy the entries into a seperate xml file and place it in the aircraft subdirectory.
Which aircrafts do you want to set up? Maybe we can cover them too.
There are no profiles like different setups for the same aircraft at the moment. You can modify the existing config (xmls are in plugins/SAM/aircraft but they get overwritten in case you update.
We might come up with a more comprehensive solution one day.
I'm not able to reproduce this. Loaded up the E145XR with SAM GroundService (door opened automatically when bus arrived and closed after leaving), started engines manually and off we go: