Staining Cedar Shed

I have a very nice cedar shed on property that I recently bought that houses a whirlpool. The top portion is roughly a rust colored color and is in reasonably good shape. The bottom has lost most of its color (it is now a light color roughly equivalent to light maple). Can someone give me hints as to the best way to stain the shed? I am a little wary of staining it when the top portion is not in the same condition as the bottom. Thanks,
JD
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