do you need to wait for 3 confirmations at the pump during 30 mins, i mean if you're lucky your tx is not queued

technically it should be just an double-entry accounting process within the company. you need a $ budget you are willing to grant for bitcoin sales. if the costumer pays with bitcoins the equal amount in $ will be moved from this budget account and the bitcoins inflow will move to an another account. this bitcoin account will oscillate in value over time but on the long run it should be not an issue.