The question is of primary importance, I'm facing the same while plotting raw and averaged sensors data.
raw data: y (a vector of length 1000)
averaged data: z (a vector of length 100)
You can define a common x-axis and plot your vectors with respect to that. I chose time and I made an average of time values for each 10 samples (10 because I'm averaging 10 values each):
time: t (a vector of length 1000)
time averaged: ta (a vector of length 100)
Now just plot the values with the same length and you'll get two graphs with the raw and averaged data, in the same plot and with the correct spacing