How long have you been on 50 mcg? That is just a starter dose. Your doctor should have tested after six weeks on that dose and increased your eltroxin. It's time to ask him for another test!
On the day of the test, don't take your levo. Leave a gap of 24 hours between the last dose and the test, otherwise you will skew the results. On a normal day, take your eltroxin with a large glass of water, one hour before or two hours after eating. Don't take it with coffee, or tea, just water. That way, you will get maximum absorbtion. Because if you're not absorbing it properly, it isn't going to work, is it. lol
After the test, ask for a print-out of the results - it's your legal right to have them, and you need them for your own personal records, so that you know exactly what's been tested and where you are with it. If you don't understand the results, ask here, and someone will be able to explain.
i'm afraid you might have to put your foot down with your doctor. None of them have much idea what they're doing when it comes to thyroid, and need a firm guiding hand. You say you're waiting to see an endo. Do you already have your appt? The sad truth is, that endos don't have much idea, either - although he might know more than your gp! In the meantime, you have to learn as much as you can about your disease - read, read, read and ask questions, until you know more than your doctor does (which isn't difficult!). You've come to the right place here, where people can help you. Don't be afraid to ask.
And in the meantime, get those thyroid levels tested so that you can get an increase. And get the vits and mins tested too, as others have suggested. They are incredably important to your well-being, they all need to be optimised - and don't let your doctor tell you otherwise!