Editing Issue (and More Research)

 I'm aware this isn't the best time to see this but only after I shot was the issue prominent on my mind: how am I going to shoot this? 

Given my story, there are two main options:

1. Shoot the scenes of the modern day and past separately, then blend them.

2. Shoot the scenes of both actors all on the same frame. 

The reason 1 is preferable is that even if I shot the entire thing very poorly (and in truth, I'm not entirely enthusiastic about the footage I do have), it would still be extremely clear what's happening when the young protagonist and father faze through the protagonist (in that the audience would be aware it's just a flashback or some sort of thought in the protagonist's head). The reason I would do 2 is because it's just more convenient. I have hardly a clue how to edit the first option, even though I'm pretty sure most films that do something similar with memory to mine shoot in that way. So far, I have a couple of shots which are appropriate to blend/be overlaid, but there's a lot of camera movement in those and I'm afraid what the finished product is going to look like. 

Moreover, and this isn't an editing issue, but I just didn't do a good job with mise-en-scene. My actors wore the same clothes the entire shoot which means I may as well throw out a good portion of shots, especially when our father is supposed to age throughout the piece. The hard truth is that I'm growing increasingly nervous about this piece. The scale isn't that large but most of what will make the idea worthwhile seems to be out of my expertise or requires much more planning than I initially thought.

Add grain to indicate our character is looking at a flashback?? Maybe it can work but it doesn't make complete sense to me.

I've also come across suggestions to use a filter to indicate the scenes of the past but that literally makes no sense. The flashbacks aren't really flashbacks but our character's current understanding of them—a recontextualization after his maturation from his childhood! That's the entire premise. I don't even have enough experience in this field to practice it because I just opened adobe and I have no idea how to even do the first step of the blending that the first video I watched told me to do. I feel stupid only trying to see how to edit this piece now, but I'm also sure I can find a way around it should it not eventually become clear to me at some point.