Although I'm guessing you want "y" to increase up on the screen as well. Not sure about that one

    translate(0,height-1);

    scale(1,-1);

Put that at the beginning of your draw.  Wrap your draw in pushMatrix()    popMatrix().  

Note that it's height-1, not height.  Otherwise, 0 is off the screen.

Here's a complete example:

2. void setup()
3. {
4.   size(500,500);
5. }
6. 
   
7. void draw() 
8. {
9.   background(255);
10.   // the old way
11.   stroke(255,0,0);
12.   line(10,10,100,100);
13.   pushMatrix();
14.     translate(0,height-1);
15.     scale(1,-1);
16.     // the new way
17.     stroke(0,255,0);
18.     line(10,10,100,100);
19.   popMatrix();
20. }
21. 
    

For what it's worth (very little), this is a mental convenience that makes the it easier to continue thinking about coordinates spaces the way you were taught.  From years of coding, I've pretty much unlearned a lot of those things.  I think of Y as going down.  I don't use percentages (I use 0-1).  Counting starts at zero.  Degrees are in radians.

EDIT: *Angles* are in radians.  :)