How to detect a long signal inside an even longer one?
Using the matched filter is right approach and typically a full length filter should be used.

One of the advantages is that  filter gain is approximately proportional to $10\log(T)$. 

If you don’t need full gain you can use a chunk of your matched filter and still have acceptable detection performance.

One technique in active sonar is to use a broken up matched filters because returns tend to be broken up. A target isn’t a point reflector. 

You can also use linearity and time invariance to break up the long convolution. Say take the first half of your matched filter and convolve it with your long time series. Then do the same with the second half matched filter. If you align the 2 convolved time series, offset by the length of the first half filter, adding the convolved time series is equivalent to convolution by the full matched filter