If Im trying to export a video to 320x240 (.FLV), does it matter what the sequence settings are in terms of size/resolution? I've tried cropping the output so that it gives me a 320x240, but it apperas to distort the quality of the image and especially my titles.
You will want your Sequence setting to match your source footage 100%. Edit, as is required.
Now, to get your output (basically "quarter screen"), just use that setting in AME. The "cropping" will take place automatically.
Good luck, and hope that this helps.