Q] Where is everybody?
A] At the end of The Headmasters, the Cybertrons and Destrons left the Earth and headed into space. It is explained in Super-God Masterforce that the other Transformers who are not on Earth are continuing their war in space, so that is where the likes of Fortress Maximus are.
Q] Do the Seacons and Sparkdash have robot modes?
A] Presumably they do (the toys did) but for some reason, these characters never transform in the series.
Q] Why do Shouki and Suiken appear in the first intro?
These two characters -who are probably with the rest of the Trainbots -were originally from The Headmasters series, and whilst they appear briefly in the first intro for Super-God Masterforce, they never appear in any episode. It is unclear why they are in the intro, and fans speculate if they were supposed to make an appearance. In the manga, the Trainbots do appear, and are used to transport the Cybertron humans on Earth to Athenia. Perhaps a similar idea was planned for the anime, but then discarded.
Q] Is the manga different from the anime?
A] The manga has some completely different stories, please visit the TF Wiki for more info about it.