This may be a dumb question, but will you really sit there to do your makeup? I had a similar setup and never used the vanity..it just became a catch-all. That space might be better utilized for more storage (drawers). If you do use the vanity, I think it should be lower, otherwise you will need almost a bar-height stool/chair.

I will use it and I can't wait to have it! Before buying my first house I always had a desk in my room used for this purpose, but then I moved in with DH and that didn't work anymore. Now, you may laugh, but currently I often sit on the counter with my feet in the sink!

If I kept it all one level I would need a counter height chair. I would get something without a back. Would that be awful?

I think it will look fine either way....if it is lower, you have a dedicated/defined area as your makeup vanity. If it is the same height, that space may or may not be used as a vanity and will just become part of the overall sink area. Only you can decide which will work better for you. A counter-height stool COULD look a little strange in your bathroom and is not the norm, but if you like it that's all that matters.