For those who are looking for a better way to time track their projects I recommend Toggl.com. It’s free if you only need the basic features and up to five team members. If you need more feature and more team members you can opt into the reasonably priced pro versions. There is a 30 day free trial for you to see if it’s really needed or not.
I like using the web app as it shows the most detail but they also have a desktop and mobile app available for you to use and it can interact with your browser and other websites.
When it comes to charging I personally use a mix of flat and hourly rates, depending on the project. If you currently price all projects as flat rates you should try timing some of them… it was a huge eye opener.