We using toggl.com to track each task. And at the end of the week we sending you detailed with a list of tasks and time, we spend on each one.
For planning, we using Trello.com. Usually, we have Planning board and Development one. On planning board, we designing features, estimating them and after that move them to Development board to start working.
When developer started working on the feature he creating new git branch and when finish - deliver Pull Request for code review by the senior developer.
Each week we sending to clients invoice with Toggl detailed report attached. So you can see what are you paying for. In the invoice description you can see developers salary, Guru fee and Company fee (we call it Society fee). So, society fee is 30%. Developers working for 17$/h salary. UI/UX team 10-12$/h.