You are almost there, your code will be default add the element to the first Customer. You need to search for the attribute id in collection of Customers whose value is 2 -
document.Element("Bank").Elements("Customer")
.First(c => (int)c.Attribute("id") == 2).Element("Accounts").Add
(
new XElement
(
"Account", new XAttribute("id", "variable")
)
);