You really don't have to create additional VFolders unless/until you find a reason to do so. Each VFolder has 200 scanlists so you could just keep adding systems and channels and just put them in different scanlists.
I tend to create new VFolders for "special" programming - like for road trips or other situations that take me to different locations. This way, I leave my home/local programming alone for when I return home.
Like all software, it can take some time to get comfortable with EZ Scan. I can say the same thing for Uniden's Sentinel. I've beta tried other 3rd party packages as well and I got aggravated with those too and never bought any (except Win500 for the PSR-500 long before EZ Scan). It's like anything else - the more you use it, the easier it gets. I've now been using EZ Scan since the PSR-800 was released and I find it very easy to use. While I don't like it, I've also gotten used to most of Sentinel's quirks too but I don't use it all that much.