First, break the overall job into individual parts, which should be obvious.
There are usually three ways I bid a job, depending on what it is.
The first is by estimated or actual time, either daily or hourly. This works well for things where you don't know exactly how long it will take you, or if you will run into extra issues. On things like decks I give them my "daily rate" and tell them I expect it will take 4-5 days, etc. Make sure you are there on time and don't leave early, don't give them a reason to feel cheated. For more detail oriented jobs like wood rot or siding repair, just bill it hourly.
The second way is by square or linear foot, if you know exactly what you're getting in to. This is good for flooring, crown or base, and you can usually make more billing it this way rather than by time or by room.
The final way which can work well if you're doing the work yourself and not paying employees or subs, is just by how much it takes to make it worth it to you. For things like installing doors, just give them a number that you will be happy with making whether it takes you half an hour or two hours.
The last way is great for jobs where there are multiples of something, as you get faster the more you do it while still making the same money per item. It is also a good way to do it when you are gaining skills, techniques, specialty tools and speed. It allows you to make more money as you get faster and more efficient without making your customers feel exploited.
To explain, picture hanging doors. If you charge $200 per door and are new at it, using chisels and a belt sander, hand nailing etc, it might take you 4-5 hours per door so you make around $400 per day.
A couple years later with experience, a router and template, cordless planer, nail guns, etc, you might go to that same customer's new house and hang a bunch of doors in 1.5 hours per door, still charge them $200 per door, they are happy, and you make a lot more money.
If you had started out charging them $25 per hour then increase it to $50 per hour, they are going to feel taken advantage of and complain, even if you are twice as fast as you used to be.