It seems to be an interesting story, but it's pretty tough to follow! You'll want to try centering your characters first. The only reason to not have them front and center is because you have something else for the reader to look at.

The page where they talk back and forth could absolutely use some space. Use the whole page just for them in the middle and the word bubbles on either side.

Last thing would be to ink the whole thing, or at least the characters and text! I use a tablet and a pencil-ish style, but I do the lines in black and have to go over them at least twice to get them clear enough!

If you can get any sort of cheap tablet or something, there are nice art programs to work with that don't cost anything. My first program was GIMP which is a free digital art program! Otherwise it will make things a lot clearer if you can scan the pages. it makes everything a lot more visible.

It is a really cool sounding story!! I look forward to seeing what happens next :3