or will it leave marks when the braces are removed?
Well, you doing that once in a while probably won't whiten your teeth all that much. That being said, if you were to whiten your teeth while you had braces, once they are off, you will find that the parts with the braces are a different shade so I would recommend you hold off all your whitening tricks until you remove your braces.
To make it easy so you dont have to brush everywhere and get in to tight spots, swish some peroxide in your mouth for about 30 seconds and that should help slightly. ALTHOUGH it doesnt taste good and I don't reccomend that you swallow it :)
Well, baking soda once or twice a week is fine - it helps with whitening, but lemon juice? Who ever told you to use that? Lemon juice contains citric acid ... it eats away at your enamel.
Having braces usually leaves marks on your teeth afterwards anyway so I don't think it'd make a lot of difference.
Ive done it when I didnt have toothpaste.