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Click the marquee tool, make the size/shape you want, click paint bucket tool, select the color you want, fill. Click the marquee tool again, move to another area, fill. The advantage of this is that you can maintain your selected size while doing other things, like creating new layers. If you screw up, you can always reselect (or press shift+ctrl+D) and get it back.
Alternatively, you can highlight the area you *don't* want filled, select inverse (or press shift+ctrl+I), and then use the paint bucket tool.
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