Hi jerseypros,
I've had a store for many years. I'm not exactly sure what you are asking about as you do not control your shipping and payments through your store. That is done globally as Bernie mentioned with Account Tab in your My eBay.
That being said, if you want to customize your end of item/auction e-mails AND your invoice...then you would look under Logos and Branding in MANAGE YOUR STORE.
It's below Item Promotion and above Reports.
If this is not what you are looking for, be more specific and I'll see if I may help you. I know my store inside out as I spend many hours in there!
Have a good one,
Susan
momoftwingles2