I'm a trans guy, but I don't really 'pass' as male (yet... waiting on doctors appointents is ****) so I have the bathroom dilemma too, it really sucks. I mostly just go with the 'I don't care' attitude and use either mens or womens depending where I am and how I feel about the place. I've come across a couple of sites with tips for passing in the mens room
Hudson's Guide: Bathroom Use & STP Devices
Urinal etiquette ? things you should know before taking a tinkle | transthetics
perhaps there's something there you'd find helpful. Are there any unisex toilets at your school eg. the disabled toilets, that you could use? I know it's not the same as using the mens, but it's better to be safe...
You're definitely not alone in dealing with this