But to answer your original question, if you're planning on doing them a little bit apart, I would pitch the correct amount of yeast for the whole batch into the first one.
Curious why you'd suggest this. It seems like, considering that a Barleywine is a big beer and is therefore going to require a huge amount of yeast, this could be a perfect opportunity to try out that 'drauflaussen' thingy that was discussed last month.
Basically, do the first 3-gallon batch and pitch the correct amount of yeast for that size. Next day, do the second batch and, since the first batch has functioned as an additional "starter" step, there should be enough yeast now present to just run in the second batch. Main benefit being only half as large a starter is needed.
Of course, chill that second batch before running in and, most importantly, like Keith said, control those fermentation temperatures!!