The new plugin will automatically migrate the deposit addresses and transactions (and therefore balances) to the new format. There will be an extensive article detailing how this works. You will not have to do anything for this, other than ensure that the cron jobs are running.
Connection to the wallets will not be migrated automatically, you will need to create wallets and currencies. This will be detailed in the installation instructions and via WordPress admin pointers. It will be easy, and if you have any questions about it you can post in the new migration support forum.
You will be able to perform these changes at any time, and you can safely revert to the previous version if any issue arises.
If you have any more questions about this, please post them at the migration support forum.