I've been music engraving professionally with Finale since 1997. This is an efficient workflow that has worked well for me over the years when engraving a full score.
Number the measures in the manuscript if engraving a project from scratch.
Add the appropriate number of instruments to the score, set up the instrument names in the margins, as well as transpositions if applicable.
Set up percussion note shapes if applicable.
Add instrument names, including abbreviated names starting on page 2.
Set up the general page layout for the size of the ensemble (page size, general size of the music, margins)
Add first page information (title, dedication, composer, arranger, lyricist, copyright information, instrument if it's for a single instrument).
Add running headers from page 2+ (page numbers, title)
Add however many measures you need to match the manuscript.
Add time signature(s) and key signature(s).
Add tempo markings, including ritardando and "A Tempo" markings.
Add repeats and other roadmap markings (D.S., coda, etc.)
Order of Entry
All notes first
Flat beams where appropriate
Lyrics (if any)
Articulations, adjusting around slurs where needed
Text expressions (dynamics and other text) and smart shapes (hairpins, 8va signs, pedal markings, etc.)
Layout and Cleanup
In page view, apply note spacing and then "Update Layout."
Distribute measures as needed for readability and aesthetics. If engraving a piece for piano, ensure reasonable page turns as much as you are able. If you are engraving a vocal piece, make sure the measures are spread out enough that syllables don't crash into each other.
If there are any instrument changes for a particular part (Oboe to English Horn, or percussion parts with multiple instruments), change the instrument name in the left margin where needed.
Clean up details page by page, line by line.
Adjust instrument staves vertically system by system to make sure no element from one part is crashing with the part above or below.
For a score with voices, adjust syllables right or left as needed to avoid crashes and show hyphens.
Clean up crashes in general – slurs and articulations, dynamics and notes (or articulations or slurs), 8va signs, etc. Slurs at the beginning or end of systems can also look weird. Fix as needed. At the same time you're doing this, make sure that dynamics and hairpins align horizontally. Clean up anything else that looks off.
Proofread BEFORE extracting parts!