dunky2, there are many options you can take. Each has it's benefits/issues. I'm not sure which products you are using and how many systems are being managed.
start from scratch : cleanest / easiest method BUT involves reconnecting all nodes again to new ePO server. You can save the agent keys from old server and import to new one. In addition you will also export policies/tasks etc and "import" all of these into the new server.
in-place upgrade : you can try this method, should be fine if all incompatibilities are resolved prior to each upgrade. i would take a full backup of epo server and database before every upgrade.
setup secondary and transfer: similar to other method but reduces some work.. so you will setup a new server, then register it with current ePO server. you will need to exchange server keys. Once that's done, you can slowly "transferring" systems/policies/tasks etc.
Having done the upgrade from 4.6 to 5.1 to 5.3, I'm now looking at transferring the systems to a new server when I go to 5.9. I've already done the client upgrades from MA 4.6 and 4.8 to 5.0.5, and am finishing the migration from VSE to ENS, so all my policies are pretty new anyway. Having said that, there are a few "legacy" (read prior admin-installed) products in there that aren't doing anything and are having trouble uninstalling, and I've got some issues with my SQL database setup as well, so I have more reason than average to not go the in-place upgrade route. Just my two cents, for what it's worth.