I am a full user of Inventor and Solid Works and I am learning Fusion 360. The problem I find is that I cannot just CREATE new cnc type joints for boxes and such. Is there something that can make these or do I literally have to design each on into both parts?
There isn’t really one answer to this. There are so many joint types, and the sizes depend on the application.
A common joint type is the box joint (also called the finger joint as it looks at a corner like interlocked fingers when you clasp your hands). When machined in production, they are usually done either with ganged circular-saw type cutters or a square end milling cutter with the axis parallel to the material plane. CNC machines like the Shapoko or the Nomad don’t have an easy time with this, so it is common to cut these joints either with rounded fingers or to cut a relief at the inside corners of the fingers so the fingers of the other part will fit.
On the occasions I use this style joint (in Inventor, and Fusio360 is similar), I will generally set the pattern up for the task as a separate part, then bring it in (using DERIVE tool) as many times as needed and use it as a tool to cut the pattern into the edges using COMBINE (see Making a fitted case for a tool for an example). You need to be careful about the alignment.
This makes it pretty fast and easy to set up.
Another common joint is the Rabet (rabbet, rebate) joint. This I just build into the model, as it is quick and easy. Not as strong as a box joint, but not bad.
There are some notes on this at: https://www.shapeoko.com/wiki/index.php/Fabrication_Techniques_%26_Hardware#Joinery
as well as: