jordanthielman:
I hear that you are not supposed to use Fritzing diagrams to draw up your circuits as they are difficult to read and easy to misinterpret. I have been learning Eagle in order to properly ask questions and problem solve on my circuits, however I get the feeling that Eagle is just for drawing up PCB boards, not drawing a schematic of an Arduino circuit
The OP has a misconception or misunderstanding here that no one has picked up on or attempted to clear up.
TLDR: Schematics are diagrams but not all diagrams are schematics.
Fritzing may be unique among similar software packages because it has 3 modes or 3 views of the same circuit. They are called "breadboard view", "schematic view" and "pcb view" or something like that. They could all be described as diagrams, but only the schematic view can be described as a schematic.
Breadboard view is the one that Fritzing is famous, or infamous, for. Forum members here hate them so much they refer to them as "Fritzies". They are brightly coloured and attractive to younger forum members, but as the OP has noticed, difficult to understand and easy to misinterpret.
Fritzing, used in schematic mode, can produce quite good schematic diagrams. Often, newbies fail to produce a good schematic using it because they don't understand how to produce a good schematic even with pencil and paper. Also they don't download suitable component symbols for the components they want to use, which is a neccessary step when using any schematic drawing package.
Eagle has no equivalent to "breadboard view". It is aimed at a more mature, experienced user base. So it can't produce those breadboard layout diagrams but it absolutely can produce good schematic diagrams.
So how is a schematic different to a breadboard or pcb layout diagram? In a breadboard or pcb layout, the relative size, position and orientation of each component is important. In a schematic, those things are not important, and the components can be made whatever size, position and orientation makes the whole diagram simpler and easier to read. The only thing of importance in a schematic is the connections, and making them easy to read and understand.
The classic example of this difference is the London Tube map. It's not actually a map, it's a schematic. The exact locations and distances between stations are not accurately represented. Only the connections between the stations is important. That's what made it easy for travellers to use compared to the true "maps" that came before it.