IIRC you can only use the cloak once, so either wait till nav 3 to cloak (before destroying the cap ship) and then autopilot to nav 4, or cloak right after launch and leave the damned thing on untill you're breathing up thrakath or hobbes ass. Uncloak and unleash a missile volley up his tail pipe. The later requires patience as you have to wait till your out of range of fighters before you can autopilot to the next nave point.
However once you are on the surface (I dont know if this is a bug from reloading the engine after the FMV sequence or not) you can cloak immediatly after you get there and avoid the enemy fighters all together until your ready to launch the temblor bomb.