There's some musical information missing here - for my answer, I assume that this is a keyboard (piano, ...) piece, with treble clef on the upper staff and bass clef on the lower:
<Image Link> and that you want to indicate that the right hand should play the two low f's:
<Image Link> I do not know much about (more complex) keyboard writing - maybe others know how it should be done. But I think attaching some text notes (m.s. = mano sinistra = left hand; and m.d. = mano destra = right hand; or l.h. and r.h.) makes clear what should happen (and yes, I would leave in the rests):
<Image Link> I tried it with cross-beaming (see attached .nwctxt file) - but first, I cannot see a way to route the lines so that it looks acceptable. And second, the Beam.hmm object limits the lengths of the stems (starting with the second note) to 20 - I never thought anyone would need more. Here, it seems, the second note of the first cross-beam would need a beam length of 30 or so to get it working more or less:
<Image Link>... however, as I said, cross-beaming seems overkill to me, here. Let me know if you need longer stems, I can most probably change that easily.
Re your question "
how to get the middle stave stems to show up without the flags", setting the stem length to zero worked for me. But there
seems to be a bug in the Beam object: The left beam suddenly vanishes if it is short than 7 or something like that. In my experiment above, it worked because the length is a little larger ... I'll look into that problem when Ihave time.
EDIT: Ah - there is a solution that looks somewhat acceptable (the nwc file is now also attached):
<Image Link>And I cannot reproduce the problem with the vanishing stem - don't know what happened there.
Lastly, I have uploaded a new versin (0.9) which has the "final stem length" limits increased to -50...50.
H.M.