I asked this same question a few months ago, and the general feedback I got was that you can really do either, but some people feel it's better to age the batch all together in the secondary fermenter.
What do you mean when you say age? Are we talking weeks or months? Also, how much trub and stuff is on the bottom of the secondary?
I mostly keg and therefore age in bulk in the keg with very little sediment. I know you can have problems with carbonating down the road if the beer secondaries too long, but I don't imagine you are talking THAT long.
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