First of all, I think you should read about Iteration in python.
Just to clear things up:
list1 = [[1, 2]] means you have list1 containing a list, which contains the list [1,2] at list1[0].
list2 = [[[1, 2]]] means you have list2 containing the list [[1, 2]].
Secondly, in order to change the value of the first item in the list, from [1,2] to [88,88], you can write:
list1 = [[1, 2]]
for item in list1:
item[0] = 88
item[1] = 88
print(list1)
output:
[[88, 88]]
Now, let's explain:
For each iteration of the for loop the variable item is assigned with just a copy of the value of an item in the list, so changes made to item won't be reflected in the list.
That is why in your first attempt, (with list1) when you iterated over the list - item = [88, 88] only changed the copy and not the actual list (the copy here was of the list [1,2]).
In your second attempt, i.e:
for item in list2:
item[0] = [88, 88]
For each iteration of the for loop, you are accessing item[0] which is a copy of the reference to the first element in item. Therefore when you assign value to it, the value is changed in the list.