Resizing panels inside of panels inside of panels...

I'm trying to organize a GUI by using a series of panels inside a JFrame. I have added panels within these panels to organize my information since I've never been able to figure out that ghastly GridBagLayout. Anyway, I've hit a wall. It seems that I can't resize an object inside of a panel that's inside of a panel. I use the setPrefferedSize method, but it just doesn't have any effect. This is true for both panels and buttons. Am I right in my assumption that there's a limit to how far into a pile of panels one can use the setPrefferedSize method? I'm using primarily BoxLayouts if that makes any difference. Any help or suggestions or advice would be appreciated.

I'm afraid the SwingUtilities.updateComponentTreeUI didn't work. When I say I'm a novice, I'm afraid I'm kind of shooting in the dark as to some solutions and problems. Let me try and clarify my problem a little bit with an example. I have JPanels A, B, C, D, E, F, G and JCheckBoxes 1, 2, 3. JPanel A is added to the JFrame. The rest go as follows:
A.add(B);
B.add(C);
C.add(D);
C.add(E);
D.add(F);
D.add(G);
G.add(1);
G.add(2);
G.add(3);
Every JPanel has used the .setPreferredSize() method to define the size I desire. JPanels A, B, C, D, and E all keep their preferred sizes. However, F and G mock me by resizing according to the sizes of JCheckBoxes 1, 2, and 3. Even though they are coded to take up a certain amount of space (which is well within the limits of JPanel D), they don't. Instead they just go to the default size, which is to allow all components within it to be visible. I have this same problem when I add other components into JPanels D and E, like buttons, other JPanels, etc. I hope this clarified more than it confused.

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