Not really sure which one this fits under...
When I use Easymod (happening less often as my number of mods are getting to be too high for it to work well), I usually comment out the COPY/MOVE commands from the mod and manually upload those to the appropriate folders. The reason I do this is because I've encountered many mods where I just get an error stating the files can't be moved. Usually because the mod is written such that the files are being copied to the same place they are rather than to the correct location. Many work fine, but it's just easier for me to ignore the COPY/MOVE commands and just upload appropriately. Except for really large mods, most don't have too many files that this is difficult to do.
I also tend to remove any lines that Easymod can't handle and do those manually if I'm using Easymod.
If we're talking about upgrading Easymod, it would be very useful to have it not fail completely when something doesn't work when updating the files (not the database). Instead of failing just because it can't find a line, it would be useful to have it write out a list of the failed sections into another file and continue on. Then, a person can manually do those lines.
*EDIT* Well, I went into settings and figured out what you were talking about. I use automated FTP and have voted as such. I also did the vote on the other one (buffer/ftp). I think I just used default settings when installing Easymod.