You can select one peak in one spectrum and another peak in another spectrum that is same one the one you select in the first spectrum while holding Shift key. By that way, you can select two peaks (one in spectrum 1 and one in spectrum 2) at the same time. Then, using al window, you can align. That is very easy. Theres another way using st window if you want to type shifts manual. Please let me know if this does not work for you.