The easiest way to figure this out is to step through the code.
In tk2dSpriteCollectionBuilder.cs, look for this line
tk2dEditor.Atlas.Builder atlasBuilder = new tk2dEditor.Atlas.Builder(atlasWidth, atlasHeight, gen.allowMultipleAtlases?64:1, allowFindingOptimalSize, forceSquareAtlas, allowRotation);
tk2d does a whole load of things to the sprites before putting them in the atlas, but all you'll need to care about is getting the padding correct for your sprite. .Build() will return != 0 if failed.