I've noticed when I press the accelerator pedal that there is a distinct 'step' where it feels like it's all the way down but will click through it if I keep pressing down, much like the kickdown function on automatics I've driven in the past. Is the accelerator on the manual transmission supposed to be like this?

It is yes, In my Octavia if you are in Evo drive mode and push the peddle to the floor, you only get 70% throttle. If you push past that into the spring loaded step,you get the full 100% throttle.

It only works in Evo mode, both normal and sport give you full throttle every time you push the Acc peddle to the floor. The spring section does nout.

I imagine this is more for (kickdown) and the DSG folk among us,but as I have never had DSG car I cannot comment.