You put everything that you modified or used in the modified files. Examples: If you just changed the speed of Titans, you will only put the GameMechanics folder, in it only the Creature folder, in it only the Creatures, folder, in it only the Academy folder, and in it only the Titan.xdb file. If you also gave the Titan Chain Lightning and changed the animation, you will do the same things with the Chain_Lightning_Hit.xdb file and the Titan-arena.(AnimSet).xdb file.
You should put the .pak file in a .zip folder with a readme file stating that you made it and what it does along with installing instructions.