A big part of my story is how the main character regains his memories gradually and it allows to make him more "human." I was considering doing it as a sort of reward effect. Complete X goal or action and have a memory regained. I also thought of having it simply come gradually and at any time I desired. This allows a more free flow and I could thus put the memories in places according to mood. I tend to like fantasy a bit more than Sci-Fi, when writing, due to the fact that I don't have to worry about debates over the possibilities of what could or could not be. Fantasy readers just tend to shrug it off as, "whatever it's magic." However, I have a series I've been working on for a while now and had an entire change of the concept. Originally I started off with a main character. Than I had a basic outline of a novella. I started falling in love with the idea of creating beautiful memories that conflict with current reality; pain, love, and struggle. The MC is put in a setting with no memories and then slowly regains them as he begins to develop into something new. After that I just had to figure out a way that I could make it all work. It's a series and my setting is a bit out there, but I wanted the whole universe to be my oyster. I came up with some crazy ideas to give access to multiple time periods and virtually any location I wanted. Then I started reading more books and came up with my own unique idea that is well... a hellova lot better and less confusing. The question I'm trying to get across though is it acceptable to interlace past memories in a story which has a completely new setting? Keep in mind that the only other human interaction will be from his memories. He's set in a survival-esque situation and it may at times break the flow of action, but it's become essential to the entire plot and eventual twist. I'm not looking at a Jason Bourne type idea, but are there any examples of a character having amnesia and then developing as the book progresses? I'm just looking for references, so I get the flow right.
If you were gonna drop in memories as and when you feel like - depending on whether these memories help the character complete a task or affect a plot point, it may or may not be an issue. To give a basic example, say your MC has to fly a plane to save his life and then conveniently remembers as he pulls the levers that he was a pilot originally - that would likely come off as cheap because it's just too convenient. I understand you likely wouldn't do something that obvious, but it's definitely something to keep in mind. As for flashbacks/memories, including them as separate chapters could work, depending on their importance and their length. My advice would actually be just to write it from start to finish as you feel led, and then go back and edit the hell out of it. This is really about structure and pacing, so there's no quick solution like "If you do A, you'll be fine."
what exactly is your setting? i didn't fully understand everything on that part, but I think I understand your basic concept. There are plenty of films about amnesia, but they're normally mystery thrillers. The Alfred Hitchcock film "Spellbound" focuses on this as a character unlocks more memories as he slowly tries to solve the mystery of a murder like a jigsaw puzzle. I'm not sure if that's quite like what you're writing, but its the first thing that comes to mind in stories about memory. You may want to watch the film if it helps, its one of Hitchcock's underrated ones too XD
I may be a bit wary of learning this stuff from a film. This is one of those things where the difference in mediums has a really huge impact. Flashbacks/memories simply don't work half as well in prose as it does on film when everything's visual. Just think of Lost - can you imagine that written in straight narrative? The break in flow would be massive and I don't imagine it'd work well either.
The setting is going to have a major theme of survival, at least in the first book, which will cause the MC stress and an intense emotions. I'm thinking the memories should come at pivotal times of these emotions or after a scene which he survives against the odds. As I said before, the memories are used to make the MC seem more human. They also serve as a away to motivate the character to struggle on -- to give him a reason to live. No convenient skills to help him, just the will to go on.
