More than likely you'll have to do it as you say (there is a full 6.5.4 package as opposed to upgrade but this is for 64-bit new installs on 2003/2008)
You can only upgrade to a "base" installation - that means 6.5.
After that, you can apply the 6.5.5 release update. (I notice you said 6.5.3, but I would gently request you go with the latest and greatest, as it contains the most fixes and I'd hate to see you have to apply more sets of release updates than is absolutely necessary. :) )