Having played with the Cartographer's Table yesterday to look at the Map Pack, I can tell you the most important thing I learned: you must exit the game completely, restart the game, then you can reload your work to be able to see any changes you have made.
Yes, it's buggy.
Also, for map size changing on you... I'm going to guess you trusted that "overwrite file" button. Don't do that. Save as a new file name. Later you can go into C:\Users\Username\My documents\My games\fallen enchantress\data\maps and delete all the old versions and thumbnails once your work is finalized.
The Cartographer's Tool is like a skittish horse, it can get you from A to B if you're patient, but it is not to be trusted implicitly. Compared to Civ 5's or even AoW:SM's map tools it is still in the toddler stage of development.
However, many people are saying that they wish that fixed starts were added to some of the Map Pack maps and I found that to be a pretty quick and simple fix saved as a new map name, something creative like "Anythys Fixedstart Tarth". (Remember you will be player 1).
If you google search for Fallen Enchantress Cartographer's Tool bugs you'll see what I mean about the limitations of the tool, but the ability to change and create maps with difficulty is certainly preferable to not having any way to do it at all!