BSBI recently commissioned Martin Rand to write a comprehensive and up-to-date handbook, covering all aspects of MapMate use from a BSBI perspective. This is a fantastic resource that should help answer almost any query you have about using MapMate! The available chapters can be downloaded as PDF files using the links below.
Update at April 2014: new versions are now available for Appendices B and C. Appendix B has some revised instructions for setting up custom queries, and there is now a separate text file containing the required SQL; Appendix C has some minor edits.
Martin Rand would be pleased to hear from you if you find any errors in the handbook, and to receive suggestions for improvement or other comments.
In places the Handbook makes use of a training database, see Chapter 2, page 2-7. The training database can be downloaded here: Training.mdb (zip file).
Martin Rand has also written an Introduction to SQL for Mapmate Users (updated January 2007), containing extensive guidance on how to write the code needed for adding custom analysis queries to MapMate. This is available via Hants Plants (scroll to the bottom of the page).