Pronunciation question, please help?

It should always pronounced if you're saying just "What?" on its own. It's always pronounced if the next word starts with a vowel e.g. "what are you doing?" etc. If the next word is "do", "does" or "did", the "t" tends to disappear in casual conversation, e.g. "What do you think?" becomes like "whadda you think?" For other words that start with "d", you should still pronounce the "t". E.g. if you said "What door is is it?" you should distinctly pronounce the "t", it would be weird to run it together as "whadoor is it".

I sometimes pronounce t as a t sound, and sometimes I use a glottal stop

I pronounce the T but whether ones or doesn't depends on where in the UK you come from which determines which accent you speak with.

I am a Wha? person. I tend to not pronounce the "T". I also say "dint" instead of "didn't". I listened to a series of lectures on language and this is normal. There is a term for it, that I forget, but many words are pronounced different than they are spelled because of this.