Much depends on where you are starting from, what skills you can apply, and how much time you have.
If the stake already has implemented some form of Geo Code areas, even though this legacy method is extremely dependent on manual work, the most expedient course might be to build on that. This begs the question of how to design the Geo Code areas in the first place, on some maps somehow. MLS provides no tools for doing that; it is completely dumb geographically. Stake MLS will report demographic analysis based upon the manually entered Geo Code values. (If you entered "Geo Code" values based upon your research of hair and eye color, MLS would report that demographic analysis, too.)
Otherwise, you might be better off exporting the MLS membership data into external geographic software for analysis. Design your areas there, import boundary building blocks based on publicly available files for such areas such as census tracts and school districts, or some synthesis of both methods.
As of this writing, the systems provided by the church for boundary analysis are pretty crude compared to the state of the art in Geographic Information Systems, which integrate databases with electronic maps. Designing boundaries in GIS is a mature art. Governments and businesses have been doing such tasks with GIS for years. Salt Lake headquarters has GIS software. Local units do not, unless they acquire their own. This is a specialized field, however, and there is a learning curve involved in using GIS applications. That course, in turn depends on the inventory of experience within the stake clerk's orbit. Someone with database skills can surely learn to use GIS.
A middle ground hybrid method might be to use GIS such as free Quantum GIS or moderately priced Manifold -- or lower-end map-display applications such as Google Earth -- just to draw Geo Code areas. Then use them as a productivity tool to assist clerks in doing the Geo Code data entry into MLS for the demographic analysis. (It's basically a tradeoff of brains versus brawn. If your clerk can write a little SQL code within a GIS system to do the database analysis, he doesn't have to do all that manual data entry.)
If you do want to use any modern mapping tools, they typically are dependent on geocoding the latitude-longitude values for each member address, so there also is an issue of how to capture that data. The church has built a semi-automated tool for doing that within the maps application at lds.org, but it is ultimately dependent on a lot of manual work by ward clerks. That ambitious task is generally treated as optional unless mandated by stakes. If your units have already been doing that, then you have a valuable asset to use for boundary work; if not, it would take some time for ward clerks to ramp up. If your stake does not have this asset in place and you are under the gun to do the boundary analysis quickly, you might just get the address geocoding done commercially. There are many ways to get free geocoding online, but they usually lack completeness and accuracy.
