You can see which battles you need to complete using the Systems menu at the console.
The easiest way to complete this achievement is to enable some cheats and then go straight to the objective. There are 4 main types of battles, Destroy the Command Center, Destroy the Statues, Destroy all buildings, and Build an Escape Pod
I recommend that for all the Ground Battles you enable Invincibility (j46p7a) and Super Speeders (b1d3w3). For the Escape Pod levels, Stud Magnet (6mz5ch) and some multipliers [x2 (yzphuv), x4 (43t5e5), x6 (sebhgr), x8 (byfsaq), x10 (n1ckr1)] will speed up the ability to create all the required buildings.
With the cheats enabled and the Systems map to guide you, just rush straight for the objective. DO not build anything unless it is on the escape pod level.
Best strategy to complete this would be to start with the Republic assault on Naboo (once it has been unlocked) and then converting all Separatist planets (in red) to Republic (in blue). This will get you Admiral of the fleet achievement.
Once that is complete, then convert all the planets (which should all be blue) to the Separatists (in red). That will get you the Viceroy of the fleet achievement.
After that, use the System map to identify the remaining planets that need to be completed on your way to 100%