Input music in small sections at a time. Two, four, or eight measures is usually a good size, but it depends on the size of the composition, the size of its sections, and the form of the music. It doesn't make sense to input a passage of 9 whole-notes in stages of two measures, but two measures may be too long for passages composed primarily of 128th-notes.
Input one staff at a time, then check its accuracy using Frescobaldi's preview function (press the "LilyPond" button on the toolbar)
Input the pitch and rhythms first, then slurs, articulations, ties, and fingerings. It's easier to correct errors with pitch and rhythm (and register!) before the extra markings are added.
To help make sixteenth-note passages easier to read, you can use double- or triple-spaces to separate beats. Such passages often feature repeated patterns; before copy-and-pasting, make sure that the pattern repetition is truly exact!
When you progress to a new four-measure section (or two- or six-, etc.), input the less difficult staff first (if there is one). This way, you will have a better visual reference when verifying the more difficult part. It's easier to see differences if your score looks closer to the original.
The same idea applies for multi-measure polyphonic passages in the same staff: input the easier part first, so you have a visual reference.
To help ensure that you don't get lost, write measure numbers in the source file every five measures or so. See the example source file to see how this is done. Even if you don't want to have measure numbers in the final score, it can be helpful to include them during inputting and error-checking.
Save the dynamics and pedal markings for last! Sometimes, they can help you to keep your place in the score while double-checking that it's correct, but I don't usually put them in with the rest of the notes, for reasons described below in the "Piano Dynamics" section.
