Problem with losing quality in exporting FLV

First I should emphasize that I am new to Adobe's products, and am learning it on the fly as part of a intelligent tutoring system design project. So I apologize for my lack of technical knowledge in advance. Rest assured I have put much effort in attempting to solve this problem on my own and by referencing this forum and other web sources, but sadly with no success.
FYI, I am using the CS4 Master collection.
My question pertains to retaining the quality of my video once I export it to .flv format via Media Encoder from Premiere Pro. My main video source is an .flv file that i have imported into my media browser. Initially I ran into a problem with the importing because it did not recognize H264 as having any media, and so I had to convert to Sorenson format to get it to import successfully. But it seems to have imported just fine without any loss of quality in the workspace. So that isn't my main issue but perhaps it is related.
I am having major issues with losing quality upon export back to .flv format - which is the format I am required to use - the video is being imbedded within a larger program and so it needs to have a smallish file size. For the life of me I cannot figure out any combination of settings that works. If I select same as source then I end up with a video that is surrounded by black borders. This may because the workspace is larger than my imported file. I have attempted to enlarge it to fit the safe margins but it hasn't helped. If I resize my output video to 640 x 480 - which is what I want - I get a shrinked video with black borders. If I crop the input to what I want I just lose quality - but I lose quality either way. I really want to accomplish this without increasing the bit rate (and thus the file size). I have tried just about every setting available and I still lose the quality. Is this just inevitable? Is there a plugin that would help? From what I can it seems that Adobe has more problems dealing with .flv than with other video formats, but I haven't found anything that pertains to this issue specifically.
Otherwise does anyone know of any other programs that can edit .flv files and offers multiple video & audio tracks?
Thanks in advance. If anything needs clarification let me know.

Ah yes I left out that detail. My source video is 640 x 480 also so the output is not an increase in size.
This is different from my sequence settings. Which is 1440 x 1080 16:9 ratio. Pixel Aspect Ratio is HD anamorphic 1080 (1.333).
I am assuming that this needs to be changed but I can't figure out how to do that (sequence settings are greyed out). Should I just start a new project?

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