Before the base is installed, you might want to paint the underside of the dollhouse. It's optional whether you want to finish this area or not. This is where the drawers and technically, once the drawers are in, this area will not be visible, until you slide the drawers out. Just keep in mind that painting raw wood is not only done for aesthetics, but also for protecting it.
Since I decided to finish this area, it has to be done in a way that will not interfere with the movement of the drawers. I gave everything one coat of good quality paint. I then lightly sanded everything for a smooth finish and made touch ups. I used spackle along the joints to fill in any gaps. I made sure that I pushed the spackle deep into the joints, so that it will not interfere with the drawers once it dries.
I then painted the side of the base sheet that will be facing this drawer section. I also gave it one coat of paint, sanded and then made touch ups. Once dry, I glued it in place and clamped it tightly.
Once it's in place, you will have to reach in with a long paint brush to make sure you wipe up any glue that might have seeped outside the joints. The joints need to be very smooth and all obstructions removed.
You can then use a paint brush or a long piece of strip wood to apply spackle to any gaps in the joints.