when i do any repairs, i put each component, and its associated screws) into a 2"x2" zip-top baggie (https://www.amazon.com/dp/B09DX8HVDV) to keep everything organized.
you're already using the ifixit guides for sizing and placement. so i don't need to explain that step to you. :)
early on i bought couple of full screw sets to have for random spares. unless you're dealing with specific ones like standoffs, a lot of the phillips and tri-lobes can be used in different iphones, provided the diameter is right and the shaft is not overly long. depending on where you get them from, full screw sets for a given model are anywhere from $3 to $9.
to get the right fit, it's either trial and error, or you can use a digital caliper/micrometer, like this (https://www.amazon.com/dp/B07DFFYCXS)