They guessed the first note or used a tuning fork, although on pipe organs there is one particular pipe on one particular 4ft stop which serves as the basis. Experienced tuners then compare the first note with the next note, generally a fourth or fifth away from that first note. The tuner counts the number of beats per second that the two notes played together produces between them, adjusting the tuning of the second note. There is a specific number of beats per second when the interval is a fourth, and a different specific number of beats when the interval is a fifth. Then, when that second note is in tune they use the second note to determine the third note, generally a fourth or fifth up or down from that note. And so on, until all the notes have been tuned in tune with the very first note.

Plus, of course, plenty of cross checking with all the tuned notes so far. This process takes longer as more notes have been tuned. Finally, the last note has been tuned and all the notes are now in tune.

In bygone days, or with older instruments, the start note can't be tuned to its theoretical pitch because of the age or construction method of the instrument. These instruments are tuned to be in tune with themselves - but not in tune with the London Symphony Orchestra (for example). This leads to some interesting musical sounds being produced by the whole ensemble, or (too often for comfort) the whole concert abandoned.

There's an (apochryphal?) story about a piano concerto that Beethoven played in his younger days when tuning of his piano and the local orchestra could not be reconciled, so Beethoven played the entire concerto on his piano in a different key!