From the terminology that you're using I believe you are using Crossfire (?). I'm not familiar with that program, and I don't think there is a document that serves as a tutorial for the use of it. However, I'd suggest you access one or both of these Facebook groups: Cruciverb or Crossword Puzzle Collaboration Directory - and inquire if there is an experienced user of the your software that would be willing to do some mentoring for you.
Those issues (grid design, fill strategy, word list management) are very important, and frankly there are no cookie-cutter answers. Each puzzle/theme/grid is unique, and a lot of trial and error goes into developing a construction process that works.