It is a good idea to postpone work on page layout until you have completed all other tasks:
|compose or arrange the notes of the song
|add annotations such as accent marks, dynamic marks, and phrase marks
After your are done writing and editing the music, then:
After you have completed all of the above tasks, and are fairly certain that you will not change the work, only then should you then work on the page layout: adding page and system breaks, rearranging measures of systems, changing the vertical spacing of staves and systems, etc. If you start working prematurely on the page layout, you may have to discard some of your page layout effort. For example, if you add some introduction measures at the beginning of the music, then this might disrupt the pagination of the entire score.
Nevertheless, Musician's page layout mechanism can be forgiving about how changes you make to the music might impact pagination. Try using the Keep Measure With Previous and Keep System With Previous options, instead of "hard" system and page breaks.