I originally posted most of this in response to another thread long ago, but was reminded about it when the topic came up today.
This is for those of you who write using Sonar and later prepare your scores in Sibelius (or who wish to do so).
I always start in Sonar, and work until a piece is complete before I give a single thought to notation. I do this because the way a piece sounds is of prime importance, so I want it to be perfect and finished before I procede.
The next thing I do is save the entire Sonar file as a MIDI file under a new name. I then close and reopen the MIDI file so that Sonar empties out all the VSTs and somewhat simplifies the track information. I then get rid of any extraneous tracks, including empty plug-in placeholders, duplicated tracks (brass overlays, extra string patch doublings, etc.)
The next thing I do is open up all tracks simultaneously in Event View mode. Using the display filter, I view everything except for the notes themselves--all MIDI control messages should be displayed. I select the entire list and hit delete. I am now left with notes only (save the file now!)
Here is when the most work-intensive part begins.
I close the event view, highlight all tracks, and open them in piano roll view. I like to keep only a few tracks visible at a time, depending on the nature of the music. I may decide to work on flutes and oboes together, or all woodwinds at once. This is mostly determined by how similar the parts are rhythmically. The idea here is to simplify the parts as much as is possible. I highlight large blocks of notes that have the same rhythmic subdivisions, and begin to quantize 100% beginnings and endings of notes, making sure I don't destroy any tuplets. I remove any overlap between notes.
Note-This step (100% quantize) will save you many hours of headache later. Just be careful that the quantize value is correct for each passage you process.
I also combine tracks that will appear on a single staff. So if I have two tracks for the two clarinets, I will move the second part on top of the first, and delete the now blank track.
Once I've simplified all the parts as best I can, I save the file again. Now I have a notation-friendly version of my music.
The rest of the work I do in Sibelius. I like to set up an orchestra template that contains all the instruments in the piece before I import the MIDI file. This is because it's easier to set it all up myself rather than to fix the guesses Sibelius makes. Depending on the complexity of a score, Sibelius may do pretty well here, but my scores get fairly complex.
Now it's time to import the MIDI file into Sibelius. I like to keep my template and the imported score open at the same time, then I copy and paste entire instrument sections from the imported file to the template.
Next I switch to panorama view and track down anything that looks unusual rhythmically. Any problems with the quantize values become more obvious at this point. It will also be easy to spot anywhere in the score where notes incorrectly tie and overlap for monophonic instruments.
The rest of my time is spent cleaning up the score. The big things are remembering to enter pizz/arco markings, dynamics, and re-notating percussion to work on standard percussion staves. I use the "set all to same pitch" plug-in on single-line percussion staves. Then I examine all the accidentals and note spellings to see if they can be improved (there are some great Sibelius plug-ins for this). The last step is working on cleanliness, pagination, etc.
After I think everything is in order, I print out a draft so I can see how it really looks on paper. Many things I won't notice on the screen, but are very obvious printed out. I mark everything with a red pen, and go back to clean it up. I usually have to do this several times.
At this point I am also listening to the work on my iPod while following the score to find anything that got missed. I sometimes also find a few things I want to change about the piece itself at this point, and mark them as such (a new doubling, changed articulation, etc). If I change something like that, I have to go back to the Sonar file to bring it up to date as well.
I have a feeling that this is much more work than most people here are doing, but I wouldn't have it any other way. I have complete control over every single aspect of my music both as it is rendered and as it is displayed. It is a boatload of work, but worth every minute in my opinion. I am always looking for ways to speed up my workflow, but never at a cost to the final output.
I hope this has given you some ideas.