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.
Like you said, a barleywine is going to require a huge amount of yeast, and given the higher OG it's not the most favorable environment for yeast growth. My thinking is that I'd rather pitch the right amount for the whole batch to make sure I had a good population of healthy yeast in there to get the job done.
If you're going to brew this in two separate batches, you may consider taking a few pounds of grain from the first batch and adding them to the second batch instead. This way your initial batch is a bit easier on the yeast. then once they're roaring away you can hit them with the higher gravity wort (which would end up getting diluted by the initial 3 gallons).