Exemplo de como adicionar dados em um arquivo XML.

Aluno.java

package expxml;

import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.Collection;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.Result;
import javax.xml.transform.Source;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;

/**
 * @author Dener
 */
public class Aluno {
    public Aluno(String nome, String curso) {
        this.nome = nome;
        this.curso = curso;
    }

    public Aluno() {
    }
    
    private String nome;
    private String curso;

    public String getNome() {
        return nome;
    }

    public void setNome(String nome) {
        this.nome = nome;
    }

    public String getCurso() {
        return curso;
    }

    public void setCurso(String curso) {
        this.curso = curso;
    }
    
    //CRUD
    public void addAluno(Aluno aluno, File arquivo) throws
            ParserConfigurationException,
            UnsupportedEncodingException,
            SAXException,
            IOException,
            TransformerConfigurationException,
            TransformerException {         
        
        if (!arquivo.exists()) {
            //Cria o xml
            DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
            DocumentBuilder builder = factory.newDocumentBuilder();
        
            StringBuilder xmlStringBuilder = new StringBuilder();
            xmlStringBuilder.append("<?xml version=").append("'1.0'").append("?>").
                append("<aluno>").
                append("    <nome>").append(aluno.getNome()).append("</nome>").
                append("    <curso>").append(aluno.getCurso()).append("</curso>").
                append("</aluno>");
        
            ByteArrayInputStream inPutByte = new ByteArrayInputStream(xmlStringBuilder.toString().getBytes("UTF-8"));
        
            Document document = builder.parse(inPutByte);
            document.getDocumentElement().normalize();     
            
            /*Cria o arquivo XML com base no objeto document.*/
            Transformer transformer =  TransformerFactory.newInstance().newTransformer();
            
            Result output = new StreamResult(arquivo);
            Source in = new DOMSource(document);                              
            transformer.transform(in, output);
        }
        else {
            //Rescreve o XML
            DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
            DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
            Document document = documentBuilder.parse(arquivo);
            Element root = document.getDocumentElement();
            
            Collection<Aluno> alunos = new ArrayList<>();
            alunos.add(aluno);
            
            for (Aluno a : alunos) {
                Element novoAluno = document.createElement("aluno");
                
                Element nome = document.createElement("nome");
                nome.appendChild(document.createTextNode(a.getNome()));                
                
                novoAluno.appendChild(nome);
                
                Element curso = document.createElement("curso");
                curso.appendChild(document.createTextNode(a.getCurso()));
                
                novoAluno.appendChild(curso);
                
                root.appendChild(novoAluno);
            }
            
            DOMSource source = new DOMSource(document);

            TransformerFactory transformerFactory = TransformerFactory.newInstance();
            Transformer transformer = transformerFactory.newTransformer();
            StreamResult result = new StreamResult(arquivo);
            transformer.transform(source, result);            
        }
    }
}