I get the best, most consistent results by scanning everything as a positive, then inverting and running levels and curves and whatnot in photoshop.
What i do is just scan everything while watching television at the least messed with settings, then go through and run an action i create specifically for each film i use in photoshop in one big batch. Once the batch is done running, i go back and adjust frames individually, but i usually only do that if a frame is over or underexposed.
Most films have a pretty similar action, generally i invert, then do a conservative levels. Usually the result is a little dull compared to a real print, so i usually add a little bit of a curve to make it pop a little. When i'm building an action for a new film i check it on a few normally exposed frames to make sure it works across a bunch of photos. Once that's done doing all the adjustments is really quick and easy.
I found when i was starting that negative mode was all over the place, and didn't get nearly as much tonal range out of anything. Add to that the fact that the "negafix" part of silverfast has a grand total of like 3 films (none of which i use), it's really slow to use, and generally futzing in silverfast does more harm than good, i essentially decided to use it as little as possible.
All in all, it's a really good scanner for the price, and one of the only ones out there new that isn't a flatbed or a million dollars. It's just quirky.