I'm new at this, but the way I quote a job is with a detailed breakdown of the materials and the labor. I'm concerned that I may be giving the customer more information than they need, but it works well for the sake of coming up with accurate quotes. It also takes some time and consideration, but when you're starting out in this business I suppose you should always dot your i's and cross your t's anyway.
For example, for a vinyl job on a vehicle, I would list a breakdown of specific items such as the vinyl, transfer tape, cleaning/application fluids, etc. marking everything up around 100%, especially since we stock a decent amount of vinyl and have to keep it stored in a climate controlled facility (plus it takes up storage space). Then I would list labor items such as design and prep time, cutting, weeding, and transfer taping time, vehicle prepping time, and application time. I sit and think about the task based on prior experience and come up with a reasonable estimate of time, then multiply it times my hourly rate.
Then if I'm not entirely certain, I refer to the contractors pricing guide, when possible, and compare it to see if my quote sounds ridiculously off. So far it's worked out pretty well. I've never lost money on a job yet, so that's always good.