I first drew a 2D layout for a box in LibreCAD. This contained a piece for bottom and top, and one for the sides. First I used lines and later used the mirror tool to clone them.
Then I imported the file into Fusion 360 by uploading it.
With that sketch as groudbase I extruded the both parts to a body. While drawing I considered the notches to be 5mm deep, with this measures you would be able to use 5mm mdf in the laser cutter. So the amount I extruded was also 5mm.
After I had both parts extruded I arranged them using the move tool. First the bottom part had to be layed flat.
And then the side part had to be moved precisely to the ground part so all edges would perfectly align. Using different views this task was way easier.
The result of this looked like this. But there were still three side parts missing. I used the move tool and enabled creating a new body out of the moved body. So I was able to easily create the other three parts and align them to the objects.
After doing that for all leftover sides I had this object. Now the same procedure just had to be done again for the bottom part.
When the final part came on top I had my little box. And this showed that my thoughts about where to make notches were all correct. With this as a base for assembling 3D objects I will be able to make more complicated objects in the future.