I work in a pretty similar fashion to Valence - blocking and choreo notes go in the libretto, then I call from score. I have varying methods of producing my calling script; sometimes I get a script and a piano score and go at them with scissors and glue, sometimes I retype (or scan and OCR) the script, scan the music and insert it as pictures into the typed script, and my latest and greatest method is to get an electronic copy of the script (retype or OCR), and then get the piano score into Sibelius (either by scanning it in - Sibelius does have its own OCR-type engine which will convert scanned pictures of music into actual music! - or by getting it from the MD if it's a rearrange, as my next musical is) and copy and paste from Sibelius into the electronic script. It's only the latest version of Sibelius that lets you do that, but it's an absolute godsend. The scanning the music as pictures works, but you do end up with a huge Word (or whatever you're using) file - I think my script for The Producers came in at something like 133mb. I'd advise using the score if you're comfortable reading music - it just means you can be so much more precise in your calling.