Thanks, and sorry about the title, haha. Unfortunately though, I don't think you understood my problem. I know the thin yellow wires mean there is supposed to be a connection but it hasn't been routed yet (actual traces aren't there), but if you take a look at the SMD part in the board, you will see that no thin yellow wires are going to it... there should be connections from resistors et cera to that part, but it's just sitting there doing nothing. Actually, one connection did go through fine which was the grounded thermal pad on the back of the chip; however, none of the actual pins are making a connection even though I'm drawing nets in the schematic.
As a second note, I did try pressing F9 to draw a new wire, but it doesn't line up with the pins. The grid is (I believe) on a 0.05" spacing, which the casing of the part lines up with, but the pins are in between the points which I can access (if i click on pin 1 to draw a wire, the wire starts in between pin 1 and pin 2).