Thank you. Don't sell yourself short. It's a bit of a balancing act. If you charge too much, you won't get business because clients can get the same service cheaper elsewhere, but if you charge too little, clients may feel you're incompetent.
As for how fees are calculated, I realized a few years ago that charging by the square foot makes no sense to me. When I design a house, I must provide the same drawings and details for my construction documents, whether it's a 2,500SQFT house or a 4,900SQFT house. A renovation/addition may require more of my time than a new house of comparable size. I use a spreadsheet with a menu of tasks, to which I assign hours for each task, plus fees for outside services (printing allowance, surveying, civil engineering, structural engineering, landscape architect, etc). I may adjust these based on the "******* tax" factor. The spreadsheet determines my lump sum fee based on my hourly rate.
By tracking my time, I can compare it to my spreadsheet and determine if I'm charging correctly for each type of job, if I'm using my time as efficiently as I planned, etc. Sometimes I incorrectly estimate my hours, but I'd have no way of knowing without measurable data.