I have... several problems. My main one is I have no idea what I'm doing
That one is better solved with a proper education in video production. The forums are best utilized to find answers or advice on things that don't appear in manuals or Help files, or that aren't covered in a formal education. They're woefully inadequate as a substitute for a proper education.
As always, the proper procedure is first learn, then do. You're trying to skip step one. It's no wonder you're having a rough go of it.
Ok, let me rephrase that.
I don't know what I'm doing in THIS INSTANCE. If people only read the first part of my statement I guess I'm not going to get anywhere, so I'll just be a tad more concise. I've made many videos before, using Premiere, and exported them successfully. This time however, and I have a feeling it's a combination of things, I'm having trouble getting the output right.
Media Encoder isn't giving me the option of of matching sequence settings which I normally use, and I've used a few different formats of export. .AVI results in poor image quality, what I've heard referred to as "jaggies" or artifacts, and therein lies my first question; is there a way to get rid of these? Secondly, using MPEG2 Blu-ray, I get the resolution that I'm keen on, but it seperates the audio into a .WAV file. Therein the second question, what's a recommended program for combining the two.
I'm aware of the tutorials, and part of self learning is watching them all. However there isn't a particular one that covers my question, which is why I posted it here.
Secondly, using MPEG2 Blu-ray, I get the resolution that I'm keen on, but it seperates the audio into a .WAV file. Secondly, using MPEG2 Blu-ray, I get the resolution that I'm keen on, but it seperates the audio into a .WAV file.
That is perfectly normal and expected when outputting for BR, unless you turn multiplexing on.
If capturing already took you three weeks and you don't know about multiplexing, you are seriously missing the basics. I second Jim's remarks, get an education first or at least study the help file from front to cover first and watch some basic tutorials.