Dollars are far more admitted in Peru than euros. I mean you can pay at markets and restaurants with dollars. Euros are not that accepted, but I think money exchange locations accept euros (in Miraflores, in Tarata street there is a m.e. that accept euros and money from other south american countries).
I have not heard about a 500 euros bills restrictions, or 100 bollar bills, in banks and m.e. But usually they don't accept 100 dollar bills at restaurants.

Just in case if you have problems changing euros at money exchages or your hotel, go to Banco de Credito, there are several branches that accept euros:

Lima:
Miraflores - Esquina Av. Larco
San Isidro - Juan de Arona 893 Esquina con Rivera Navarrete
Lima downtown - Jr. Lampa 499 esquina con Ucayali
Plaza San Martín (Lima downtown) - Jr. Ocoña 102

Cusco: Av. El Sol 189, Cusco

I don't know about comissions, I guess there shouldn't be a high difference, but not sure.