Something I found confusing is that I couldn’t do it on the inventory screen when in the store, I had to go to the backpack inventory.

Thanks

In the square at night instead of Barto's shop

No.  You can only use one scroll on an object at a time.  It would seem you can replace the enchantment but they don't stack.

You see their weaknesses even on Badass-mode

I also equipped 3 of them at once and the weaknesses were all marked based on success level:

grey for "doesn't appreciate that" 

green for "excites ... a little"

orange for "seems to enjoy it" 

red for "moans with excitement"