Use the version 6 upgrade installer. There should be a radio button somewhere in the early phase of the installer that tells you something like use previous serial number, or something along those lines. Make sure that is checked and then install. You'll have to enter the old v4.x serial and then the new one (the really long one).
Keep in mind. XPress 6.x was not designed for Leopard and Quark does not support it on Leopard. It will run very cludgy and buggy on Leopard. There is no "patch" to "fix" it for Leopard. Secondly, if this is an Intel Mac (and all newer Mac laptops are) then XPress 6.x will be even slower because XPress 6.x was written for PowerPC (Motorola) chips and not Intel chips. The app will be running through Rosetta which is Apple's translator fron Intel to PowerPC. Apps running through Rosetta are slower because the code has to be translated.