So I finished the render and despite a few drawbacks during the process, it looks gorgeous. During the render. 2 of the computers had turned themselves off in the middle of the night, which was kind of irritating because I had to restart the render from where they left off when I came in on Thursday morning which meant I had to delay the editing till it was finished. But after a couple hours it managed to render the whole scene beautifully and I was ready to render.
The rendering stage was a long and irritating process, when I imported the audio and video they some how were not sync with each other, which was strange seen as I had animated to the audio in the first place so it would. So to fix this I had to go through it and speed up a section of the audio so it would keep up wit the video, I mean the audio sounds a little higher but it works well.
The next problem was probably the getting the 2D thought bubbles into the premier. It proved to be difficult because when I exported the scenes from TVPaint they had a black background, instead of being transparent. To fix this I put the scenes into after effects and added a mask to area I wanted to be shown, making the rest of the area transparent. And to make sure the thought bubbles looked like thought bubbles, I messed around with the feather and opacity settings to make the bubbles look more cloudy and foggy than just a plain white image.