It is very simple to do but you have to know the proper process.
If you want to create a customize template for the welcome email then you have to create it first from System -> Transactional Emails , Now add a new Template , create it and save it.
Now go to the System -> Configuration. then Customers -> Customer Configuration ,and then "Customer New account options"
change the Default Welcome Email, Confirmation Link Email, Welcome Email with your template.
Now your welcome mail will send with your template.....