I'm assuming that you're making this for print. Automating the little boxes is actually quite easy using InDesign's built-in "Step and Repeat" function, which was added in CS3 or CS4.
Create the first little box, 1 cm square (or whatever) with no fill and a .25 point stroke.
Press Ctl-Alt-U
(Mac Cmd-Opt-U
) to bring up the Step and Repeat dialog. Enter 1 cm (or whatever size you specified) for the Horizontal displacement and 0 for vertical. Turn on Preview, and enter the number of repeats (not the total number of boxes).
Group the set to make it easier to move around.
Repeat as needed.