Hi Pavel,
I don't fully understand your question, but I can answer a portion on how to create square of different size. You can use decsg to create geometry using coordinate information.
Here is a small example for creating square with 0.6 as edge length.
% Coordinates
lowerLeft = [0 ,0 ];
lowerRight = [0.6 , 0 ];
upperRight = [0.6 , 0.6];
upperLeft = [0.0 , 0.6];
% Geometry matrix
S = [3,4 lowerLeft(1), lowerRight(1), upperRight(1), upperLeft(1), ...
lowerLeft(2), lowerRight(2), upperRight(2), upperLeft(2)];
gdm = S';
% Names
ns = 'S';
% Set formula
sf = 'S';
% Invoke decsg
g = decsg(gdm,ns,sf');
% Import g into model using geometryFromEdges.
model = createpde;
geometryFromEdges(model,g);
pdegplot(model,'EdgeLabel','on');
Regards,
Ravi
