What preferences are stored with a document?  

    MusEdit stores the following properties (or preferences) whenever a document is saved:

1) Version number of MusEdit used to create the document
2) The document window's size and location relative to the main MusEdit window frame
3) Default fixed length of staff lines
4) Preferred symbol size (large or small)
5) Autosave parameters (type (character count or time), and count of chars or minutes between saves)
6) Preferred scrolling parameters ( lines / scroll, delay per scroll, repeat scrolling, sound on)
7) Whether to:
       -show line labels
       -show bar count
       -show note values on tab lines
       -show pitches on tab lines with alternate tunings
8) Read only status
9) What line types to show
10) Whether to show chord diagrams
11) Starting page number for this score
12) Default action of up/down arrow keys (move within staff or from line to line)
13) "Keyboard sets cursor" status
14) Which toolbars to show ( Main toolbar, Extra toolbar, Symbols toolbox, Status bar )
15) Whether to make a backup file each time the document is edited
16) Default type of Tab (4, 5, or 6 string) and Bass Tab (4, 5, or 6 string) lines
17) Default tuning to use on Tab and Bass Tab lines
18) Whether to show tab pitches on Tab lines
19) MIDI parameters (eg. speed, looping, marks, instruments, etc.)
20) Default text font, staff text font, tab font
21) Whether to show chord variations
22) Print size, orientation, show size alert, keep groups together
23) Margins and units
24) Whether to show page breaks
25) Page numbering style, font, and text
26) Chord name font and color
27) Chord diagram size
28) Rhythm line font and color
29) Tab line spacing, tab digit font and color, tab digit position adjustment 
30) Whether to show Ad-Tab symbols, and what style

More may be added in the future....

Note that all these properties are stored with each document, and independently from document to document.  This means, for example, that if you are in the middle of editing a score you may want to have all the various toolbars showing, you may want the arrow keys to move within the staff, and you may want all line types visible.  If all those things are true when you save that document then they will be true the next time you open that document too.

Suppose you've completely finished editing a score however.  In this case you may want it to be Read Only, you may want to hide all the toolbars, the symbols toolbox, and even the status bar (since you don't need them anymore, and this way you maximize screen area), and you want the arrow keys to move the caret from line to line (actually this happens automatically when the document is Read Only...).  If you save the document with all those properties set then the next time you open that document the toolbars will disappear, it will be Read Only, etc.