You're probably referring to assembly code ... I find it best to devise a working algorithm before I start editing ... That means I actually write the code in an accompanying text file, including the bytes that make up the commands, before I even start editing. That way I can visualize all the bytes that are there and make sure that the algorithm doesn't use too much space.
I feel you, because I've been there (as teenager) and I know what are you saying very well ... back then I was using any piece of paper that happen around me and a pencil (so I can easily delete/change), including a bus ticket or toilet paper :D
But then after I got a macro assembler (which for that time was equivalent of miracle), I felt like the world is opening for me ... like when you have observed the world from a small window, and suddenly you go out. Only then you can really experience it, only then you can really feel it and maybe understand its different then what you have imagine trough that small window ...
How much it opened you ask? Before I could write only small things, hack lives in some games. But after that ... (well there is a learning curve) ... I made music editor, graphics editor, vector graphics and what I consider my jewel in the crown - a game similar to my fav arcade "City Connection". All done from scratch, no internet, no books to find algorithms, no friends to ask (in that time most people didn't know that computers existed).
Ops that was a little bit personal, but I see a good potential and I hope to open your eyes to see how much more you could achieve with a right tool. Speaking of which there are number of macro assemblers for SNES - xkas, ca65, bass, wla-dx. As far as I know, xkas is most used but quite buggy and not friendly for patching. The only one that I know and use is wla-dx, not the most popular, but here is the opinion of fellow hacker that has tried several:
That said, I actually went with WLA for my Super Famicom Wars translation in the end. It's the only 65816 assembler I know of that both has pretty decent "patching assembler" features and uses a decent linker which can automatically put code and data in sections you've defined as free.