I have googled my issue and it doesn't seem that I can do what I want to do without paying for a 3rd party app. Hopefully someone from shopify will see this post and feedback to the developers (as I have seen on previous comments on this issue). I also use Etsy and their shipping profile is far easier to use - set a shipping fee and have the option to add an extra per extra item.
I sell small items and can post up to 5 items in the same package at the same price - yet shopify wants to charge 5x the postage. There needs to be an action whereby you can click on "use 1 shipping rate per transaction".
Whether I go on weight, or set fee per item, I can't set my shipping fairly for the customer, it either leaves me out of pocket, or charges the customer unecessarily :(