If I'm working with footage that are different sizes, I usually always start with a background node set to the size I want the final frame to be. Then I merge the elements in front of the bg node and place them accordingly. this way when I do a filter or merge it back on, it all lines up fine.
Additionally, I set the alpha of the bg node to 0, but if you're adding fire, you can just screen it back on or whatever.

- added bg
- fix_1.PNG (575.87 KiB) Viewed 1124 times
EDIT: Looking at your flow again, I see you have things going into the BG input of a merge and that merge going into the bg of another merge. You can just remove that merge with the empty FG input and plug it right into the BG of the other merge. Ive attached two images to demonstrate

- this doesnt require the BG node, but still isnt as straight forward as the other method
- fix_2.PNG (572.28 KiB) Viewed 1124 times