Your assumption in the second bullet point is correct: that answer does not apply to your situation. The linked question is discussing separate but electrically equal analog and digital ground planes, which is a technique used to reduce electrical noise, not to provide galvanic isolation.
To answer your more general question, you should either use multiple different symbols (you may be able to rename the net for the 'gnd' symbol in Eagle to create different nets; it's a while since I used Eagle), or use named nets for your separate grounds.
Your schematic as shown won't work as intended, however. The isolated side of your optoisolators is powered from a power supply that's (presumably) referenced to the ground of the Arduino side of the circuit.
If you want each of the four circuits to be isolated from each other as well as from the Arduino, you will need a separate power supply for each, and four grounds (plus the Arduino's ground). If you only want to have isolation between the CCFL and Arduino sections of the circuit, you will need a single isolated power supply for the CCFL side - and a single ground in addition to the Arduino's ground.
In every case, remember that you can only use power supplies and signals referenced to the same ground as that part of your circuit.
I will start with a shift of terminology here -- instead of "grounds", we have "returns" -- namely a power return and a signal return. The power return is the easy case -- it should be a star topology with the star point at the power supply output, tying to the signal returns of each board at a single point in turn, and also to the chassis ground at a single point.
Now, we have the RF and processing boards to deal with. Each board has a signal return, which is handled through a ground grid at a minimum, if not a full ground plane. This return is contiguous, even on the RF board, and also is interconnected between the two boards alongside the digital signals passing between them.
The digital board can be laid out freely, provided the loops are kept small. This is not true for the RF board, though, which needs to have a layout that is strictly partitioned between analog nets and digital nets -- there should be an "analog area" on the board that has only analog signals, and a "digital area" on the board that has only digital signals. The return currents will then proceed to stay with the signals they are paired with, thus keeping them separated without the need to do any ground plane splitting.
Finally, connector shields need to be returned to the chassis ground by the shortest path possible, and there also needs to be a "bridge" between the chassis (I/O) ground and the signal return located with the I/O signals going to the outside world. (ESD/EMI protection devices, as well, return to the chassis aka I/O ground.)
For more information on this topic, I recommend reading Henry Ott's fabulous book, Electromagnetic Compatibility Engineering, and in particular, Chapters 16 and 17 on circuit board layout.
Best Answer
Given your level of experience, I suggest you focus on making a single low impedance ground. Separate analog and digital grounds never benefit digital circuitry. If they are not done correctly, they also do not benefit analog circuitry. So just ground everything together (no separate analog and digital ground). Use boards with continuous solid ground planes. You can also make an artificial GND plane on a single layer board using copper tape.
If you have to run wires from board to board, make half of the wires GND. In other words, for every signal that goes from board to board, there should also be a ground wire. For every power connection that goes from board to board, there should also be a ground wire. Twist each power or signal wire with its dedicated GND. This will save you a lot of trouble.
Each board should have room for a large bulk capacitor of at least 220 uF. This is in addition to the 0.1 uF per power pin and/or whatever is recommended by the chip vendor.
Order a kit of cable ferrites so that you have it ready just in case you have unexpected noise problems. The board-to-board wires can be routed through the ferrites to suppress high frequency noise.
In the schematic, place small resistors in series and small capacitors to ground on the analog inputs coming back from the reflectance array. Basically you want to be able to make an RC low-pass filter at each input. On the layout, place these RC components close to the actual analog input. Make sure you have an array of different resistor and capacitor values on-hand so you can tune the cutoff frequency of the RC filter.
Good luck! Have fun.