There are several things to remember when considering which bathroom to use: 1. How well you pass, 2. The environment of the place (you are more likely to be ok in a gay bar than a more conservative setting), and 3. How comfortable you are. When I speak of passing, I am talking about how likely other people are to identify an individual as their presented gender. I tend to fairly easily pass as male, but for some others it is harder.
Most transgender individuals use the restroom of the gender to which they are transitioning because that is who they truly are. Whether you are trans or any form of genderqueer, you must always be aware of the people around you. You are more likely to be assaulted over which bathroom you choose than almost any other situation you will encounter. People are protective of their bathroom space because it is so private. Always keep in mind your own comfort level in any situation, and if you feel uncomfortable at all, take a friend with you if possible. If anyone else has any advice regarding restrooms, please post it in the comments.