"how can I add the values into an array?"
Obvious; cheat!
give the checkboxes values that represent the indexes in the array.
If you have 1,2,3 vertically and 1,2,3,4 horizontally, then the top left corner would have value 1;1, and the bottomright 4;3
After receiving the post data, simply split the values back into coords and insert into the array
list($x,$y) = split(';', $aCheckboxvalue1);
$aValues[$x][$y]=1;
or something like that.
A forum, a FAQ, email notification, what else do you need?