you can use avisynth at any time during the amv-making process, but some things are better done early (like de-interlacing/IVTC-ing)
avisynth has a command called AviSource() which you can use to work on your finished video.
as far as the best script, it varies from source to source. you may be able to find something in the suggested scripts thread or in the old
amvwiki.
generally, you'll probably be doing IVTC, smoothing and sharpening (in that order) and maybe cropping & resizing but again, it all depends on your source.
if you could upload a 1-minute sample somewhere (avi or vob preferably the latter) I can give you a suggestion as to what should be done