The HDMI cables you purchased will be just fine. No need to waste you money on "Monster Ripoff" cable.
As far as the speaker wires go, what you should mainly look at is the max distance/placement of your speaker to"gauge" (pun intended) the awg requirement.. If the runs will be less than 40-45 ft., 16awg should suffice. Longer than 40-45 ft, I would use 12 awg. The basic 100ft of 16awg they sell at monoprice for around $12 will do the trick. Banana plugs are opional based on speaker connections like binding posts.
And as far as the Sub is concerned, you can just connect the digital coax cable to either the L or R input on the sub. They are both the same for a single connection. Some require a splitter like this 1 below, but not your R-12. At least I am pretty sure it does not...