Border crossings are a fiasco. The best way to do it is to hire a border guide. They typically charge about $10 per person to jump through all the hoops with customs, immigration, and vehicle permits. The better border stations have cafes nearby where us gringos hang out and wait... and wait... and wait some more. Here we are waiting for our El Salvador vehicle permits. It took us 3.5 hours to cross from Guatemala into El Salvadore.