Depending on the market, I prefer to bill by the hour.

If you have something really complex that takes a while, like compiling code, etc. you can bill that separately (equipment usage) if you have a second computer that you can use so you stay busy, or if it is running overnight. Or you can just tuck it into your normal fees if it isn't so much.

It also depends on what is standard practice in your industry.

of note is this videos for making sure you get paid:

The Vendor-Client Relationship in real life situations