I know that what 'Scrts' shows is a little advanced and you do not need to go that far.
I would say choose a HDL and begin to learn. I personally like SystemVerilog or Verilog. Just like VHDL, they are languages which are designed to describe your circuit using formulas / boolean math.
I would also say learn how to use the simulator included with Quartus, Modelsim. It is an industry standard also available with Lattice FPGAs and Xilinx FPGA and can handle SystemVerilog and VHDL. IE, learn to work there and then put your HDL code into Quartus where you would just need to define the final IOs, then you will have far less trouble adapting to other vendor's FPGAs as only the final steps will differ.
I have many Verilog beginner to advanced sample codes on this site. More of the later ones include Modelsim test-benches, though, those are a little more complex. NOTE: A testbench is a piece of HDL code which in your case would simulate what the ATMEAG IOs would be feeding your schematic/main HDL code including additional clock and other peripherals, and, Modelsim would follow those instructions and plot a logic analyzer scope of what your HDL fpga design is doing over time. Modelsim basically contains a built in compiler like Quartus, but, it compiles and simulates your design within a second making code edits and debugging quick. It is also possible to set Quartus to send your complete design to Modelsim after a compile, but, I consider working like this backwards unless you are specifically debugging an IO timing issue which a complete design.
Google for websites which give you example verilog/vhdl code to see what feels more to your liking.