The developers of Half-Life accomplished this by putting an invisible marker in both levels that acted as common reference points between the two levels. They then made an exit area in both levels that looked identical between them, and put some "change level" triggers in that area (the triggers can be in different places in each level). Then whenever the player touched the trigger, the game would load the new map and set the player's location in the new map to the same relative place as the old map, using the markers mentioned before as common reference points between the two levels. The result was a seamless transition between the two levels.

If you don't understand what I'm saying I can create some pictures that explains the whole process in simple terms.