To change the pixels per meter (or whatever unit you would like to
use) you can set canvas.ppu (pixels per unit) property as shown below
from either the code editor or the Python interpreter. The default
value is 16 pixels per units.
>>> canvas.ppu = 30
This way when your 90x30 sprite appears in Mekanimo (make sure that
canvas scale is one, you can set this from the View -> Zoom ->
Originial size menu, and see the scale in the status bar) and you
create a rectangle by tracing it, you would end up with a 3x1 unit
length rectangle.
When the canvas scale is one, sprites appear in their original size,
when you have a scale factor other than one then Mekanimo scales the
sprites accordingly.
Zooming does not change the actual dimensions of the rigid bodies that
would be passed to the solver (in this case box2D) but just the way
they are displayed.