There are several options for handling checkouts when the automation system is down.
Paper—write down the transactions and key them in when the system is back up.
Scanning into a document—scan the patron and item barcodes into notepad, wordpad or other text processing software, and then copy and paste, line by line, into the system when it is back up. All of the circulation PCs have this type of software installed on them.
If the system or a library is going to be down for an extended period of time, use the Offline Circulation module of WorkFlows. Instructions are available here.
When the system is down, do NOT discharge items. Discharging offline causes problems because the system will attempt to fill holds, transit items, etc., once the transactions are processed after coming back up, but the item may have gone elsewhere.