1. Find a piece to transcribe. This is frequently the hardest part, but keep the faith! Someday a beautiful, intelligent, awesome piece will wander into your life, and you want to be in the right place emotionally to put a ring (binding) on it.
2. Find a digital copy of the score. This is sometimes challenging, but increasingly less so.
3. Print the score, single sided, on decent paper. For the piece I'm working on, this step burned through 180 pieces of paper. Evidently I'm a tree murderer! Why would I print single sided and waste so much paper? Well...
4. Put the printed pages back into the feed slot, but upside down. On the other side, print blank music paper on every page except for the last. I get my PDFs of music paper from http://people.virginia.edu/~pdr4h/musicpaper/. This is surprisingly difficult, and if you don't flip the stack correctly, you'll print on top of the music and you'll need to throw away the whole stack and you'll be haunted forever by the ghosts of innocent trees who perished so pointlessly. I suggest making a mark in a known location on one of the pages before step 3; it will help you in the flipping process.
5. Print one more page of music paper. This goes at the front of the stack.
6. Put a ring on it. That is to say, go to Staples and have the whole stack ring bound. You could probably go to a variety of copy shops to get this done, but there's a Staples near me. Make sure it has a see-through cover, that way you can identify the piece.
7. Congratulations! On facing pages, you have a bite-sized chunk of the full score, and a pristine sheet of music paper on which to write your transcription. Imagine the convenience!
8. Write the transcription. I usually use a pencil.
But now I'm stopping to think: when people ask how I write transcriptions, they're not usually asking about physically writing out a score; it's usually about how to conceptualize music in a way which is physically satisfying at an instrument, sonically satisfying to a listener, and intelligible on paper having been written down "with a pencil." That's an interesting question I can't answer. Instead, I extensively answered the more boring question. Ooops.