I always ask for a break down of costs. For jobs like this there are typically at least three main categories.
Labor
Materials
Permits/inspections
The labor may have two subcomponents where one item is the time to do the actual work and the second is time to get the paperwork sorted out for permits and potentially attending inspections. The labor cost associated with the actual work being completed could then be divided by the amount of hours you expect it to take to arrive at a dollar per hour figure. Realize that some time will be required to get to your location and even though they aren't billing you directly for that time it is part of their cost. If the dollar per hour figure exceeds $250 you are definitely getting screwed, and in most places 100+ per hour is above normal in my experience. You can and probably should ask the contractor how long they expect this project to take them to expedite the understanding of the labor aspect of the project.
Materials can be a flexible number as sometimes the parts required might change once the job starts but it shouldn't change by a huge percentage.
Permits and inspections should be the same from each contractor. Always a good idea to check with the relevant authority to make sure that you aren't being screwed by not having required inspections done or any other number of ways this can go wrong.
On longer runs it is always a good idea to hear what the electrician is thinking for the path the conduit/cable will be taking and that will help you understand any significant variances in labor. You may choose a contractor because you like their approach even though it costs more to take that approach it might look better or cause less issues with future maintenance items. For example, if the easiest path blocks the water heater from being removed easily, you might want to pay extra to not do that. (made up example, but could happen)
I shop around and am a very capable purchasing person, electrician and mechanic which provides me the leverage to realistically question people on the work and cost required to accomplish many tasks. Any service provider in those fields should have a solid understanding of their labor vs materials breakdown and if they aren't willing or able to reveal that breakdown you should seek out other vendors. It isn't about negotiating with a vendor, it is about finding the right vendor who isn't trying to turn your 1 hour job into a full day pay check. Travel time is a real thing, and that is a consideration, but try to find someone who is near by especially for those small jobs.