Sibelius makes foreground analysis very easy to notate indeed. Follow these steps:
create an ordinary piano score and input the music as usual
use the "Layout/Instruments and Staves" dialog box (press I on the keyboard) to add another piano system
copy your music onto these staffs
remove all articulation - you can use the Advanced Filter to do this quickly and easily (CTRL+SHIFT+ALT+F)
change half and whole notes (minims and semibreves) to quarter notes (crotchets)
Now comes the clever bit ...
Go to "House Style/Edit Staff Types ..."
Create a NEW staff type with "5 lines" selected (it will then be based on the standard 5-line template)
Change the name to "Schenker"
In the "Other objects" section of the "General" tab uncheck "Barlines"
On the "Notes and Rests" tab, uncheck "Rhythms" and "Bars rest"
Click on "OK"
You are now ready to apply this new staff type ...
Go to "Create/Other/Staff Type Change/Pitched" and you should find your new Schenker staff type
Apply it to both the new staffs and all the rhythmic notation will magically disappear!
If your extract is short, you can tidy up your analysis by applying the "Pitched/No lines (hidden)" style after your last note. This will hide the rest of the staff, although you may need to delete stray rests
You can now use the following to add Schenkerian notation
Stems and beams from the "Create/Lines" dialog (press L on the keyboard)
Flags from the "Create/Symbols" dialog (press Z on the keyboard)
Use the "Create/Text/Other Staff Text/Small Text" style as the basis for chords and labels and then change to something like Times New Roman 14 with bold for chords and not for elaboration labels. You will need to add carets above the Urlinie numbers as separate characters.
Middle and background analysis
The principal is the same but do not input the music. Instead do the following:
Using the time signature dialog (press T on the keyboard) create a single bar with roughly the right number of beats for your graph (e.g. 34/4)
Delete the remaining bars
Input the notes you need, using quarters and half notes (crotchets and minims) as appropriate
Apply the Schenkerian staff type and use analytical notation as above
The way to do this is to use the "File/Export/Graphics" dialog.
For everyday use in essays and handouts ...
export the file as a "BMP Window bitmap" - the default settings are fine but uncheck "Create Subfolder"
open the file in Paint or similar, "select all", "copy" and then paste straight into your word processor
you can resize the image by dragging the corners
For web use ...
save as a bitmap as above, but for larger graphs you may want to use a lower resolution (ca. 200DPI is what I use on SchenkerGUIDE)
use an image handling packagae such as Paint to resave as a JPEG.
if you are coding the page yourself, you will find that most servers are fussy about case, so you will probably need to refer to the image with the file extension in capitals (i.e. <img src="imagename.JPG">)
For publishers ...
save as a "TIFF bitmap" but use higher resolution - I usually use 1200DPI
it is usual to keep the same staff size for all examples so ...
... before you start, make sure that you set the margins of your Sibelius document to that of the publication or otherwise they may not fit
this sometimes means that you will have to break graphs into two and it is best to know this at the beginning