When our year end accountant imported our year end into Caseware it had all our accounts as department first and account second. They now have a difficult time searching our accounts because the account numbers look like this 99-8020 instead of the correct way which is 8020-99. Is this something that we could have changed at the import stage? Did this happen to anyone else?

This is an option on the Caseware import. Suggest to your accountant that they read the Caseware manual!

Is it possible to import year end adjusting entries from Caseware?

You can import batches into Adagio Ledger, then post them to the prior year, if Caseware can export the adjusting entries to Excel or a CSV file.