As it turns out, I can have a combination of the two. There is a good open source project, LatexInWord which I recently discovered. Now I can keep the formulas I was using but have more control over layout of pictures. The interface is good - all one needs to do is press Alt-L to insert Latex. Also, I can have this open side-by-side with Lyx in view source mode, or another editor, and copy and paste. (There appear to be similar macros for OpenOffice, like this.)
Of course, I'll still write my actual papers in standard LaTeX, but for my personal notes, this should work well.
Tonight I wrote a quick macro to be used with LatexInWord. It prints out the LaTeX source for all of the formulas in the document. I thought this would be useful to have for archival purposes (in the future I might not have LatexInWord or Word so a plain text copy is good). This is basically my first Word vba script, but it worked when I tested it.
Sub ExportLatexAsText() Dim strRes As String Dim i As Integer Dim newline As String newline = Chr(13) & Chr(10) i = 1 For Each currentShape In ActiveDocument.InlineShapes If currentShape.AlternativeText <> "" Then strRes = strRes & newline & newline & "Formula " & i & newline strRes = strRes & currentShape.AlternativeText i = i + 1 End If Next Selection.Text = strRes End Sub
You can add this to the document under Macros. Just start editing an existing macro, and when you're looking at the source, put this subroutine in.