The goal of the masari campaign is to wipe out the purifier, so you have to battle your way across the continents until you reach it. To invade areas, you just move into them (your little ship will fly over), like you are doing there with Novus territory.
Certain heroes will move faster, Zessus for example, and certain fleets (again, Zessus) are cloaked when they go in. If a territory you're charging into has basic defenses, your units will take damage as they are entering the territory, putting you at a disadvantage once the battle has begun.
Cloaked fleets are pretty sweet, but they don't get builders, so unless you rush and wipe them out fast, it won't look good in the longrun. I'd say stick with your big fleet, rush if you can (some bases have no anti-air whatsoever), and call it good.
Finally, you can move to South America from the top left part of Africa. To build a base on an area you have conquered, click the square with the bars on it and select the type of base you want. The first will boost your global resource rate, the second will allow you to build units there, and the third will increase your maximum amount of research (still caps at 6, however.)