1. If you're having trouble with a particular song, feel free to drop me a line and I'll have a listen. Believe me, you won't be the first person here to do so. I'm completely self-taught, but I've developed a very good ear (even if I do say so myself lol) and I'd be happy to help. And nope, no magic bullet, unfortunately. You just have to keep at it.
2. I don't have this particular problem myself (unless it's something overly complex) but there are programs out there that will slow a song down so you can more easily make out rhythms and notes. I don't use any, but I've heard good things about Audacity.
3. I can't speak for anyone but myself, but here's my tabbing process:
Step 1: I tab out any notes I know for certain, that I've been able to make out just by ear.
Step 2: I go through the song, riff by riff, making sure what I've already tabbed is correct. If I can't make out a certain note, I tab what I THINK it is, as kind of a place holder.
Step 3: For songs where I'm not certain, I'll look on youtube to see if there's an isolated bass track available. If there is, it's simply a matter of transcribing it. If there isn't, and I'm still having difficulty, I move on to…
Step 4: I look up live performances of the song. This is kind of a last resort, though, because I tab only recorded versions, but a great many bass players don't play the same notes live that they do on the record. Still, even when they improvise it'll be in the same key as the original recording, so at least then I'll have an idea of where on the fret board to limit my note search to.
Step 5: If after all this I'm still not completely sure, I just go with my gut and stick with the placeholder I tabbed the first time.
I'm pretty sure there are at least a few of my tabs which aren't 100% accurate, but as much as I will pore over a song and play it repeatedly, sometimes note by note if I have to, I'm confident that even if they're not perfect, they're really fuckin' close (LOL) and I can rest easy knowing that I've at the very least given anyone who wants to learn the song a good jumping off point.
EDIT – seems Sid beat me to it. I could have avoided writing all this just by quoting him and adding “What Sid said.”