The hard part is recognizing the video issue you have and figuring out which filters would work best. Since some anime have different video issues, there is never an "always fits" solution. IMO, it's always better to under-filter than to over-filter. Especially if you are working with a single anime source since you won't need to adjust multiple anime to get more consistent looking video.
Unfortunately, I'll have to point you to the guides, but here's what you need to get started:
AviSynth - What it is, how it works and why you need it
VirtualDubMod - What it is and how to use it
and from the version 3 beta EADFAG:
Improving Visual Quality and Compressibility
Depending on how old your sources are and what they are, you may not need to do much of this. Most newer anime don't need much processing beyond
de-interlacing or IVTC. Some cleaning may be useful for improving compression and
resizing is almost a must.
Older anime need a little more filtering, but don't go overboard. Then there are certain exceptions where the companies involved messed up in producing the DVDs (ADV's Full Metal Panic? Fumoffu, for example has rampant dot crawl), or were working with older analog master tapes and exhibit many classical analog picture issues (AnimEigo's original Oh, My Goddess! DVDs were produced from their older production masters which were copies of the Japanese original production tapes and show rainbowing and washed-out colors among other issues).
Most downloaded sources should already be cleaned and processed, so in a way, they may be easier to work with. Major downsides are that they are compressed for easier/faster downloading so video quality may not be as good as DVDs. Not to mention that most of these videos are TV captures which may not be of the highest quality in the first place. Using fansubs also have the issue of having subtitles to deal with (and the appearance of subs in an AMV are almost never a plus in most people's opinions). You'll also probably have to deal with various codecs (DivX, WMV, H.264, etc.), containers (MKV, MP4, OGM, etc.), and some software incompatibilities along the way that make it work in your editing program.
It may help to read the guides as you are doing your video prepping. Even today, I find it useful sometimes to have EADFAG open to reference as I'm processing footage.