Im seeing that the control bits come from our c1 - c6 bits. Im curious if this is read left to right (c1 is zx, c2 is nx,..) or vice versa. Also is this read from the input instruction or from the output of the d register and I can manipulate the address there?
The c1 through c6 are bits in the C-type instruction, see Sec 4.2.3. While they are strongly related to the ALU control bits, they are NOT a one-to-one mapping -- it's slightly more complicated than that.
As to whether the control bits come from the instruction or the D-Register, the answer to that is pretty clearly spelled out in Fig 5.9.
As for manipulating the address, what address are you talking about (RAM or ROM) and what kind of manipulation are you talking about?