Scratch

My experience:  if I *display* variables in a project and then upload the project the variables stay where I put them.

But if I hide the variables in a project (and display them *during* the project) then they go to their default placing.

But a quick experiment shows that you can hide variables the same way you can hide Lists: create a sprite that will cover them.
        Have that sprite "go to front" and it will cover the variable or list.
        Then when you want the list or variable to be visible during the project, "hide" the cover!  :-)

From experience I know it works with lists online.  (I didn't upload my little experiment with variables to test it but it worked fine on my computer.)
        Here's a project where I used a chest of drawers (!) to hide a list until it was time to display it: http://scratch.mit.edu/projects/Larry828/878822.

And maybe people will show us other ways, too!  Good luck!