the nsvtools end up in C:/NSVSTOOLS or wherever you tell it, the only file in there for encoding is nsvenc.exe
nsvenc.exe /config
the nsv settings need to be the same for each file or the channel de-syncs, so here are my exact settings (screenshots inc):

the only one to change here is the Volume Multiplier.. sometimes the source .avi's are different volumes.. you can adjust this multiplier to normalize each .nsv file's volume by ear.. people have actually complained about one episode being quiet and then jumping up to turn down the volume on the next episode because its too loud.. so i've been trying to keep the files consistent
click NSV Encoder Configuration

make it look like this hehe.. i'm new to the mp3/nsv encoding, but i know it has to be CBR (constant bitrate) and i'm still on the fence about stereo at 32kbps or mono
under VP61 encoding options click Configure and make the following screens look like this:
General Tab

Advanced Tab
Settings Tab is irrelevant
alrighty now just go to the NSVTOOLS folder and try encoding something:
> nsvenc.exe /idle /FR=29.97 "c:\input.avi" "c:\output.nsv"
(/idle is just more processor-friendly, can try it without as well) (/FR= is frame rate of course)
that's pretty much it. you can click on a .nsv file as it is being created and winamp will play what there is of it so far without breaking anything
the only hard part really is keeping the volumes pretty much normalized from nsv to nsv and making sure to watch through each file to see if it slipped out of sync near the end or anything.. it can get very flaky