You could bill via the Blesta API, as all public model methods are supported.
Something to note about manual invoices in Blesta though, if you're going to generate these manually. You can enter the hourly rate in the unit cost, and hours in the quantity. You can use a quantity of something like "1 35/60" to represent 1 hour, 35 minutes, which should simplify billing for hourly work.
I would love to build a project management type of plugin for Blesta to simplify this, or maybe the ability to import invoice items from CSV.