Heels are really something that you have to experiment with to find out what works for you, and when. I wear heels frequently, but I generally don't have them on for more than 4 hours at a time. I wear anywhere from 2.5" block heels to 4" stilettos.
The comfort level depends a lot on the support from the exterior (I find stiletto booties more comfortable than strappy stiletto sandals, due to the fact that there is more external support for my ankle) and the type of heel (block heel is way more comfortable than stiletto). There is also the matter of how much cushioning is in a particular pair. And recently I've come to appreciate that some shoes have the arch in the "magic spot" for your foot and can be worn for much longer. All of this knowledge comes from trial and error, so it takes a while and can be expensive.
I have high-heeled shoes that are comfortable enough that I could walk around the mall for a couple of hours without any pain, BUT I find that it's a nuisance to wear heels if you are going to be walking a lot. You can't take as long of a stride, so it takes longer to accomplish things that require covering large distances. So if I am going to be walking all around the mall, I choose to wear flats or very low heels (say, 1") so that I can be more efficient with my time.
In your situation, if you are taking the bus, I would wear flats if you have a long walk to work once you get off the bus. You can cover the distance more quickly in flats, and you won't have to worry about damaging your heels by getting the heel stuck in a hole in the concrete (I've damaged heels by walking on poorly maintained sidewalks).
If you want to try to wear heels more, my suggestion would be to start wearing them on short errands, maybe to the grocery store, to a restaurant with friends, etc. You could also wear them to the mall if you're not in a hurry . This will give your feet time to adjust, and it will help you figure out what styles and brands work best for your foot.
