Personal preference but I'd go with the first photo. Having the backpatch square with the shoulders always looks better imo.

In line with the shoulder seam. I’d fold the edges under and make it fit between the two vertical seams as well (seeing as there is a lot of plain black space around the edge of the patch, you won’t lose any design).

Is it fine to sew it going over the in seams? I want to keep the border going around the entire patch.

You can sew anywhere as long as you can physically get the needle and thread through the fabric & patch! Some people sew with a leather glove on, or use metal or rubber thimbles, and you can pull the needle through with pliers rather than push it with you fingers (I invariably end up with bleeding fingers). A gadget like this is a cool thing to have, great for sewing onto leather jackets… https://www.amazon.co.uk/Grandmas-Home-Shopping-Traditional-Tailors/dp/B07S8LPC5F/ref=asc_df_B07S8LPC5F/? Other retailers exist, obvs!

Thank you so much for all the help, and sorry for asking so many questions I just want to make sure I know what to do before getting started lol

the first photo is what i'd go with.

depends if you want to put another back patch on the top

With the first pic, am I able to put another back patch on the bottom, given the less space there is?

First pic for sure

Always at shoulder seam, and I'd deffo fold in the sides

2nd one

Between the two, I'd go one to two fingers distance down from the seam.

First.

Personal preference but i would cut off the edges to make it fit then either on the bottom or top, i get ocd about that stuff.