Hi, Andrew nice work!
Since you are using the web based eda tool, I generaly do not have any problems with them. It's very simple and having great integration with the pcb/eletronic component firms, but I suggest you still need to learn KiCAD,
There are few benifit about kicad.
- it's open sourced.
- it has a great supported by the eda/keyboard community.
Most of open sourced EE project are using kicad as their tools, and some of professional still prefer it to some commercial EDAs like EAGLE, Altium.
there are many learning resource for kicad, one of most popular one is the Ai03's Keyboard Guide
You may follow it to know how to use kicad. Kicad also has a lot of open sourced footprint libarary.
I add datasheet about ATMEGA32U4-AU, you can check your pins, reading the datasheet maybe very overwhelming in the first place, but I still recommanded to go through it. It's very benifitcial for you in the long run since you want to get into eletronic desin/EE. And other datasheet follows the similar priciple.
- Please rewire your pcb in kicad.
I think your pcb works, but there are few things need to be improved.
If the wire are too close to the edge it may break easily, but it just a
minor things to notice, generaly it does not affect overall functionality.