1. I need to add descriptive page numbers (e.g., Project Description p.1
or C-1).
if you mean page numbers at the bottom like c-1 then a bit of ERT as follows
would do it:
\cfoot{\textbf{YourChoice\ -\ \thepage}}
this basically means page numbers come out at the center of the footer space
with something like YourChoice - 3 for page number 3 in section YourChoice.
You have to ask for package fancyhdr in this case.
2. I cannot separate my references cited (using BibTeX) from the document,
so I have to open it in Acrobat and delete, the body of the proposal, but
then I am stuck with screwy page numbers.
Cant work out what you mean here. Is it that you want the references to be
a separate document?
In that case you may want to open the sort of document you want and add in
ERT \:
\nocite{*}
That will print out everything in your bibtex file and whatever text you
have put into this document.
You will of course have to put in the Bibtex generated references in the
usual way.
Hope this help to sustain you in the world of Lyx and that you find its
worth it.
samar