You could use a package with a price of 0 and then use config options to set the amount of time that's being purchased. Some people just keep track of time, and bill at the end of the month. Doing it that way, you'd create an invoice for the time manually and you can use fractions for quantity to represent the time.. for example:
Best way to bill hourly consulting services?
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Do you have any idea if hourly billing will be coming soon?