Originally Posted by MSOE_HomeBrew
so the extra head space in the secondary won't cause any problems?
I rarely use a clearing vessel ("secondary") but when I do, I make sure to match the size to the batch. In other words, you want a 5 gallon carboy for a 5 gallon batch to minimize headspace, especially if you are going to let it sit there for more than 2 weeks or so.
In primary, you need the headspace for the krausen and because the co2 is coming out, oxygen can't get in. In secondary, though, it's different. The beer is no longer producing co2, so you lose the benefit of the "blanket" of co2 that is in the headspace. A 6.5 gallon carboy is fine for primary, but not for secondary.
The other choice, as mentioned, is to skip using a clearing vessel anyway and bottle the beer out of primary in three weeks or so.