If your agency have your visa approval letter already, you do not need to apply one more, just urge them to send it to you.
In case they (for some reasons) do not want to send you or you need the letter for specific purpose, you can apply with us.
Double application is no problem, the problem is you have to pay 1 more time for service fee. At the airport, the Officer there will track the code in the new letter and they issue visa for you. To get visa you have to pay them stamping fee, see at:
http://www.vietnam-visa-service.com/inf ... a-fees.asp I hope the above information is sufficient for you. If you need more information, do not hesitate to ask for more.