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Payments collected outside Chargebee (cash/check/wire transfer,etc.) are termed as offline payments. These can be easily tracked with Chargebee.
For customers paying offline Auto Collection has to be turned OFF. On every renewal, invoices will be auto-generated in Payment Due state. On receiving the payment, just hit the Record Payment option on the invoice details page and the invoice status will move to PAID. More on this here.
When you don't have a gateway supported by Chargebee, just let Chargebee take care of the invoicing and handle the payments on your end as discussed above.
Furthermore, you can consider using our APIs to automate the offline payment management workflow. Because manually marking the invoice as PAID can be cumbersome on a large scale. More information here.
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