I've been using the trainer and editor with Long War with no issues so far, just make sure you're running both trainer and editor as administrator. I had an issue with the trainer's options not working the other day but I started running it as administrator and now it works fine.
I also highly recommend using the Barracks options to permanently modify your characters so you won't have to re-modify your squad at the beginning of each mission.
which trainer version are you using? i try almost all xcomEW trainer but not one work. even the editor. already try administrator. i have the latest long war and the latest xcom