I don't think there's a right answer to this, pjtiling. Some of it is guesswork and some bitter experience. Most of the big materials you can cost and then add your markup and then you know you'll need a lot of Silicon, LSX, pipe, connectors, etc. so I just add about £200 for a typical bathroom for all those bits. Then I just imagine my way through the project and estimate how long it will take me and my assistant to complete those tasks. You have to build in a contingency, say 10%, to cover the "unknown unknowns" and then I tot that lot up. It allways looks expensive to me but I guess quality costs.
My quote is then submitted as a "capped" quote so the customer knows the she will not have to pay more than that for the scope of work detailed. And in the end I allways charge less than the cap so everyone's happy.
Most bathrooms cost about £5K to complete but some can be done for £2.5K and one cost £18K !