Run the meleeSP.bat to play through single player with melee weapons. The meleeSP.bat file should end up in your GameData folder and the meleeSP.pk3 should end up in your GameData/melee folder along with all the other Melee Mod files.
It is best to *not* have other pk3 files in your base folder besides the ones that came with the game, as those may conflict with the Melee Mod. This mod requires that you have Jedi Academy installed with the 1.01 patch and that you have installed the Melee Mod. This mod works with the Melee mod released by Slice, Dice & Mince. This mod will make it so that every lightsaber in the game is replaced by Melee weapons from the Melee Mod.