I merged your posts. Please do not make multiple posts in succession.
If no one replied you, edit the new information/question into your latest unreplied post.
For known values, they're in the save structure recorded by Bulbapedia..
For unknown values, compare the save files using HxD. (note: you gotta align the blocks in correct order first)
If comparison impossible, do trial and error.
See which half of the save actually has the change, then keep doing halves and halves until you can narrow down which block has the value. Finally, compare that block for before and after, to see which offset(s) has been changed
I feel as though the bulbapedia page explained it sufficiently
I don't understand what you are trying to say. What "highlighter"?
In regards to your save B consisting of nothing but 0xFF, I'm assuming you only saved in game once or something?
To be completely honest, I nowadays use PKHeX to fix checksums.
Once again, the checksum fixing is in the bulbapedia page:
erm..
It basically means it's an area that has the data you're looking for.
Whatever the data is, that's the area that has data in it.
In any case, I don't understand why you're doing this. PKHeX probably is able to edit whatever value you seek.
If it is for practice, sure go ahead, won't stop you.
Rather than ask so many questions, you probably should take this one step at a time.
Figure out for sure how to do one thing, then move on to the next point. I suggest:
1. Learn how to identify which save is the more recent save (because the game loads that one. Whether Save A or Save B is the more recent save, isn't fixed)
2. Learn how to identify the blocks.
3. For starters, locate the block for money (based on bulbapedia's guide)
4. Locate the offset for money (based on bulbapedia's guide)
5. Fix the checksum for money's block
6. Fix the checksum for the overall save.
If you cannot get past these, you probably won't be able to make any other edit.
As it was said that Ruby/Sapphire's Money isn't XOR'd against the Security Key, I recommend you try to edit a RS save first.