Hey vjeko, welcome to the forums!
The editor is designed so you can change stats and stuff, but you need to use it - and save your changes - before you load up the game. Don't use it whilst playing a game. And don't make changes and then attempt to use a previously saved game either.
Also, if you make changes, the auto-updater will incorrectly identify your files as being "out of date" and will attempt to "update" them by overwriting your updates with the original files. You'll will therefore have to stop the game updating if you decide to mod the game. We'll announce whenever a "real" update is available on the forums though. You'll unfortunately just have to reimplement your mods when this happens though.
What changes exactly are you trying to make anyways? The ships are not currently fully implemented, and i'm personally working on an overhaul of all of their stats, build costs, upgrade paths etc. There's over 400 ships that I need to go through or add though, so it's gonna take me quite a while.