After spending a couple of months discovering what DOESN'T transfer well via Gedcom files, I am steering away from using the description fields in Ancestry or FTM2012 which gets merged with the place field in gedcoms. I have also discovered that many custom facts get lost in the gedcom transfer as well.
I like the idea of being able to quickly identify the top of the line surname - or at least the Ahrenfadel ancestor who connects an individual to my family line. I will have to give this some more thought and play with the gedcom transfers to see what works well in all directions.
For me personally, I found myself with a ton of married women whose maiden name was unknown. I quickly discovered that leaving the surname blank was a huge mess trying to figure out which "Mary" was the one I needed in the master list of names. The trick I finally came up with that transfers well in gedcoms and shows up in the master list of names is to enter the married name in the surname field and then in the SUFFIX field enter the phrase (Married). Since the suffix field is unused for women, this doesn't interfere with any other data. This has been a fantastic fix that allowed me to quickly find the correct person and also allowed me to identify several duplicate individuals in my tree.