When composing for timpani, mark the required tuning at the start of your piece, and indicate changes in the score. Some composers will even make a little chart of the actual pitches in headless mini-notes – but I’ve found that it’s easiest just to write them out as technique text above the staff, in ascending order.
In the excerpt below from the timpani part of my harp concerto, I write out the tuning of all the kettles at the beginning, even those which are not going to be used right away. Right after the last note of bar 18, I indicate the change of the Bb kettle down four semitones to F#, and the Eb kettle up a semitone to E. Then I give the player seven and a half bars of common time at 72 bpm (about half a minute when you throw in the fermata) to tweak his tuning pedals. Of course, not everyone uses these markings. But if you leave them out, your timpanist is going to write them in anyway – so why not be courteous and put them in? It’s just another mark of professionalism that will help the rehearsal and performance of your work be as smooth and trouble-free as possible (or maybe better to say that fixing little problems like this gives everyone more time to work on the real issues).