So how exactly does the standard arduino/linux hybrid work actually? I guess what I'm asking is can it be used like a regular arduino with all the same functions plus wifi? Or are certain things that come easily on an uno more complex on the YUN due to it's unique architecture?
Try a Google search for "introduction to Arduino Yun." There are videos and blogs all over the place and they can explain it better than me.
The Yun is a lot like an Arduino Uno on the mcu side. The other side is Linux like a Raspberry Pi. The wifi is on the Linux side. The two sides communicate with the "bridge." For example you can have the Arduino take a sensor reading and write the result to the SD card on the Linux side. That reading can be manipulated, uploaded, etc. by a script/program or access via http as the Linux side runs a web server.
Try some research, you'll learn all about it quickly.