When you add the new version of OmniFocus to your Applications folder, if the old version is still installed you will be prompted to either Keep Both or Replace OmniFocus 1. Selecting Replace only replaces the app — your data is stored separately on your computer and will not be overwritten. The first time you open OmniFocus 2, it will prompt you to either Keep Data in the Cloud or Keep Data Here Only.
Were you syncing OmniFocus previously? Selecting Keep Data in the Cloud will automatically configure sync, and also download your database from the server if you’ve previously been syncing OmniFocus 1 or any of the iOS versions.
Never set up sync before? If all your previous OmniFocus work was done offline, choose Keep Data Here Only to either import the local OmniFocus 1 data or create a brand new database (you can always set up sync later).
If you had previously been storing data in an Archive, the first time you Move Old Data to Archive, once you select a date range and confirm, OmniFocus 2 will offer to migrate your existing archive from OF 1.