The problem I have is that when I convert a document using Pandoc from .docx to .tex, the tables get messed up. Is there a way to use pandoc that will retain the proper table formatting in .tex?
.docx table formatting
.tex table formatting after conversion
booktabs
package gives some excellent advice on well-formatted tables. If you really need identical (rather than superior) formatting for some reason, you may need to resort to hand-tweaking. TeX is a powerful system; few conversions will be perfect.