Hi Speedy Bob,
I own the Scan Dual II also. Since the film holder goes in horizontally on this model the way that you can make sure that it is emulsion side up is that when looking down from above the image should be reversed. You can also look at the writing at the edge of the film and this should also be backwards. This being said I've read a lot of debate in the Usenet newsgroups about how important it is to scan it a particular way. The general consensus for users of this model seems to be that it doesn't really make much difference. I personally scan it as I just described but I have tried it the other way around and it looks the same.
I'm actually scanning using the full resolution of the scanner (2820dpi) at 16-bit (this can result in 50-60MB files). I forget where right now but you should be able to set this as the standard output. I would strongly suggest using the Standard Scanning program and not the Easy Scanning version since it has a lot more features. You may also want to check out Vuescan software at http://www.hamrick.com
since it supports this scanner and does an excellent job, especially with negative scans. If you do a search here you should see it mentioned by quite a few people. I'm using this software almost all the time now. I don't bother with any of the built-in colour correction options and I then do all my cropping, colour adjustments, and assorted tweaking in Photoshop 6.0 instead before downsampling to about 950-1000 pixels. If you don't have PS6 then you may need to scan with 8 bit output instead. I then do my final sharpening (after downsampling) and save the image as a .tif format throughout. When I'm finally happy with the image I resave it as a .jpg with NO compression (quality level 12 in Photoshop). I used to scan at 1410dpi but found my results improved significantly when my initial scans were done at 2820 dpi instead.
Feel free to e-mail me (check my User Profile) if you have any other questions or want any suggestions about scan settings. Just don't ask me for the registration code for Vuescan as another Airliners.net user has done in the past! Ed Hamrick's software is great and he deserves the make a fair living from it.