Hi @Simon Holman - I've split up your questions a little bit:
1. When migrating VM's to Azure, can you set them to be managed disks?
Currently not during Migration, you'll need to finish the Migration process for the Virtual Machine/Network, then you Storage Account.
After this is finished, you can start the process of Migrating the VM's Disk to Managed.
2. Is the "Replication Storage Account" in the wizard the final storage account or only a replication point?
On Migration, a new Storage Account is created with the same data, and the Classic Storage is removed from your Subscription.
Storage Accounts should be Migrated separately, after the Virtual Machine has been Validated and successfully Migrated.
3. Should that be a standard or premium account as all examples I've seen show it as standard?
The Migration won't change the Storage Account's type, only the Deployment Model it sits on (ARM), but if you'd like to upgrade your Disk to Premium, you can do this after you've updated it to a 'Managed Disk'.
For additional details on the Migration process, please feel free to review the ARM Migration Overview here: https://learn.microsoft.com/en-us/azure/virtual-machines/windows/migration-classic-resource-manager-overview