what i did was looked up where the file is loaded into the code that the GUI uses to load the variables, then just did ".include myownuservars.asm"
i just use that for variables and leave the default variable file and the GUI list empty.
it will still automagically shovel you the default HUD variables there if you leave the default file in, but you can just delete them and run test.bat to compile your game instead of the test and compile button of the UI that loves overwriting hand-made changes
alternatively, you can simply comment out the original uservars file to ensure the default variables wont be returning.
also, when you do this, you will have to make sure you also initialize the variables (set their default values) correctly.
by default, user variables are stored on
GameEngineData\GameData\Variables\UserVariables.asm
and the Initialization file is stored on
GameEngineData\GameData\InitializationScripts\hudVarInits.asm
hudvarInits.asm is included in InitLoads.asm that's located in
GameEngineData\Routines\Basic\InitializationScripts\InitLoads.asm
UserVariables.ams is included in MemoryMap.asm located in
GameEngineData\Routines\Basic\System\MemoryMap.asm