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.