according to the EU we must send invoice to apple
No, it's not "according to the EU", it depends on which country you are in. But yes it is true that in some countries you are required to always generate invoices and that is why Apple provides this address in Ireland.
would be fine?
Yes.
should I write in invoice the payment that I receive from apple? or the price that I sell in store?
I think Apple don't care what you write in the invoice, I doubt that they even open the envelopes.
By far the simplest thing is to send an invoice for the amount that Apple have actually paid you, in your home currency, after you have received it. Anything else involves tracking multiple currencies, rounding, and other complications. Your objective should be to do whatever is needed to satisfy your local tax and other accounting rules.