I would strongly suggest you do not use the NiMH set-up that this guy shows.
He assumes the diode to make voltages compatible, but with a 4V solar cell and an average diode at rated load you get 3.1V if the diode happens to be of the normal PN type and uses 0.9V at the measely 200mA he calculates. But most diodes at such low current will be hanging closer to the 0.7V mark.
0.7V drop would give 3.3V, which is 1.65V per cell peak, which is not good. Not to mention that at a lower current where they start to fill up, the diode voltage might lower and you'd get 3.5V total, making 1.75V per cell. Which is very extremely bad.
To add to that CC-CV charging a NiMH is not the best way to get the longest life span ever recorded in history. The best, still relatively easy, way is Delta-Peak, for which you need at least an op-amp and a couple of transistors.
The reason this is all of no interest to him, most likely, is that he uses LiIon and a special LiIon charger/conditioner board for power packs.
Although his LiIon set-up isn't great either. He assumes that no defect will ever occur in the solar power collection and that the battery will thus always be recharged, but if for some reason the power drain is more over time than the sun can re-supply over that same time (in the winter, for example) his booster will keep working till the LiIon cell is 0.9V. 0.9V for a Li-Ion means absolute death.
Glossing over all those details, assuming it would be a good idea to use the NiMHs as in that Instructable (which, really, really, really, it isn't), you put the booster in parallel with the battery, so that it can always convert the voltage at the battery into the 5V you need. It doesn't matter if the power comes from the battery or the solar cell, if the sun is shining a little, maybe half comes from the sun and half from the battery, if the sun is shining a lot, all the energy will come from the solar panel and the panel will charge the batteries back up as well. When it is night all the energy comes from the batteries.
Putting the booster, solar and (PROTECTED) batteries in parallel just ensures absolutely continuous power to the Arduino (as long as the batteries are still alive, which may be years, months or weeks as the case of these instructions may be).
A diode added to the solar cell may well be important if the protection circuit doesn't take care of that, standard use-outside-solar-cells will actually often drain current away from your battery if there's no sun when you don't add some form of "one-way traffic" like a diode. Just as a small after-thought.