This workflow works for me very well on my LS9000. I prefer Vuescan over Silverfast or NikonScan, the latter is not fully color managed and appears to use profiles that only it can access. For negatives I scan as positives and invert in Photoshop, as descbribed by Ian Lyons here:
http://www.computer-darkroom.com/tutorials/tutorial_6_1.htm then assign a working space like ProPhoto.
For slides, I import into Photoshop with scanner color management turned off, choose "leave as is" (don't color manage), a little noise reduction, capture sharpen, assign a (custom) profile, then convert to a working space (Ekta). This works for most positives, however older Kodachrome can present an extreme color cast problem that may be corrected with an altered custom profile that compensates for this.
Andrew Rodney has a chapter on scanner profiling in his book "Color Management for Photographers" including a section on finding your scanners optimal settings.