Firstly change the following systems from Separatist (red) to Republic (blue):
• Ruusan Moon, Naboo, Christophsis, Quell, Dead Moon of Antar, Vassek, Coruscant, Tatooine
Coruscant and Tatooine unlock after completing the Hostage Crisis and Castle of Doom bonus missions respectively. This unlocked the achievement for me.
The following systems were are already Republic (blue):
• Rishi Moon, Ryloth, Malastare, Rugosa, Geonosis, Saleucami, Maridun and Florrum
Now all of the systems can be converted to Separatist for the Viceroy of the Fleet achievement.
As noted there are 4 main types of battles: Destroy the Command Center, Destroy the Statues, Destroy all buildings, and Build an Escape Pod. Use the Invincibility and Super Speeders cheats on all of the ground battles, with the stud multiplersx2, x4, x6, x8 and x10) cheats when building the escape pod.
Destroy the Command Center - Ignore everything else and head straight for the command center, destroying any ray shields or shield generators protecting it.
Build and Escape Pod - Ignore the bases with shield generators to begin with, and concentrate on the vacant plots - I normally found there were 2 or 3 empty bases which makes a good place to start. Next, move onto the bases with a couple of building on them, as you only need 6 or 7 bases to be able to build the escape pod.