Number one tip would be to not overthinking it.
And yes, worrying about ink color is overthinking it!

Default mode for any printer or form editing program is normal black ink and there's no reason to use anything else. Especially not any silly bright colors or anything like that.
Applications also shouldn't be "overorganized" with a ton of tabs or things like that. Put everything in order and if you want, you can split it into the logical three sections: sponsor forms, applicant forms, relationship proof (as they appear in the checklist). We used those really big paperclips for this - one on each of the sections. We had a cover letter for the last part that was relationship proof that listed all the things we included in the order it appears on the checklist and we indicated what documents are for what requirement from the checklist basically.
But you can also just simply put everything together in order and leave it at that. These agents have seen thousands of all sorts of applications and between not organizing at all or totally overcomplicating it, the former is better as it makes it more simple for them. This is why they ended up making that rule regarding no stapling and the like - it just makes it harder for them to arrange everything the way they like.
This is a bit confusing. You should do and put what the checklist asks for, of course. But if the checklist asks for, I don't know, documents that show common address and you have six of those, then put six instead of just two. No harm in giving more of what they're asking for, as long as it's reasonable and it doesn't go over their limits (if something says "at least two", you can put more than two; if it says "max 20 photos", put no more than 20 photos).
If you're currently living together, then you don't need to send communication stuff. I understand that feeling as I was in that situation as well: my sponsor and I had been living together for four months when we applied, following four years of long distance that included talking to each other on the phone every day for hours and texting all the time. We had enough communication proof to drown the agents in, basically. We didn't send a single thing as it wasn't required. If they need it later on, they'll ask for it.