[kylekohlmorgen]

If you can mash the whole batch run the total wort volume off into a couple of carboys and boil it in batches.  Blend it together and pitch.

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.  You probably want to get the second one in there before a couple days though.

This seems to be the easier method, but I wouldn't let the un-hopped, high gravity wort sit overnight. You'll have a stinky sour mash going by morning.

If you've got a fresh yeast cake lying around, just boil, cool, and transfer one half at a time. Long day, but it will net 5 gallons of BW.

You can also do as you said and space the brews a few days apart. Just make sure you make an adequate starter for the 1st three gallons, add the second batch at high krausen, and keep control of your temps!