Little bit of a confusing question. But Im really looking for learning some low level programming. Thing is, Dev boards like Arduino/Etc. really hide alot of whats going on.
MIT puts all the resources for their Computation Structures class, 6.004 online. It's essentially an Introduction to Computer Architecture class that's very focused on project-based learning.
The OpenCourseWare version is here. I would particularly concentrate on the labs, particularly 2, 3, 5 and 6 which take you from building an ADDER to and ALU all the way to a very simple processor (the Beta).
The link to the most recent course materials is here.
I remember when I took this class as being the first time that everything "clicked" in terms of understanding how simple logic gates and electrical components could translate into the complex machine I was using to simulate it. Highly recommended resource.