@Symphoni - These are some brilliant questions, I'll answer them to the best of my ability for you!
Essentially, you are correct. SOLIDER was made as a version of a bio-weapon to be used as an extended tool in the wars. You're fighting creatures and SeeR factions [other men] just as your leaders and betters tell you do so. It's through the plot workings and decisions of the characters that will influence the next course of action. When the role play starts officially, we'll be going to put down a particular SeeR group that has been trying to gain a foothold in Galbadia and try to gather more followers and sympathizers.
Through the course of the plot and story, the characters will gradually learn about the dark secrets carried within the government and how they were actually made. As SOLDIERS are unaware of the experiments that were done onto them during their time in Fort Lullin. They'll also discover the reason why they decided to make SOLDIERS and their purpose, other than just being merciless killers and warriors.
The Aeons are fused to the character through series of injections and experiments, consider it almost as being purposely infected as well. This is how SOLDIERS are made. They had many years of research in breaking down the Aeon cells and bodies enough to begin a proper formula used to enhance them into what they are. In result, SOLIDERS adapt and gain with the injections power that are considerably watered-down and tame when compared to what the Aeons used to be.
Through the story and progression, the characters will get stronger, tapping further into the powers and difference that makes them SOLIDER and possibly coming across the Aeons they've been fused with when they discover the truth about their creation.
Hope this helps!