which neural network topology to learn correlations between time series?
It depends a little on what kind of correlations you're looking for. Are you expecting a correlation that is present at each time step/window, or a different level of correlation per time step/window? Are you doing a classification or a regression task? Sometimes predicting the next value involves classification, but I'll assume you're looking for regression for now.

As a starting point, try feeding each of those sequences separately as input to a recurrent neural network (start with a basic LSTM and pare it down if it's overkill). I like your suggestion of overlapping windows. 

For example (pseudocode-ish):

series_1 = 1, 2, 3, ..., 100

series_2 = 5, 6, 7, ..., 200

input_1 = Input(series_1,       window_size)

input_2 = Input(series_2, window_size)

layer_1 = LSTM(input_1, input_2)

final_layer = fully_connected(layer_1)