Static Sludge
I thought you were supposed to always have it on anti alias? or was that the line work(correct me if im wrong there comes a day ill need to know color as well) and whats spot black shading?
When working with stuff for print, you should be working at resolutions so large that there is no effective difference in smoothness between aliased and antialiased lines. In fact, aliased lines at a high resolution (600dpi+) can make for sharper prints in B&W, which is why comic artists often scan their B&W art at 600dpi+, aliased black and white (no grey pixels at all).
I work in colour, which is printed at a significantly lower resolution (300dpi) than my working resolution (600dpi), so it doesn't make a difference whether I use aliased or anti-aliased lines and shapes. Having them aliased makes them easier to select, fill, etc.
Even though I work with aliased tools (even for my lineart and shading, not just my flats), once printed or reduced in size for the web, everything looks fine. If you work at a low resolution, then the aliased lines might show up in the web/print version (still not an issue for flats though, since your lineart would hide those edges).
I have some other reasons for working with aliased colours and lines, but in short: as long as you're working at a large resolution, it doesn't hurt.
Spot blacks are solid areas of black (or whatever ink you use). Spot black shading is shading done with solid areas of ink/black rather than colour or tone.
In practice, when I have inked lineart/shadows in a colour comic, my inks and spot blacks aren't black, but some other colour to fit better with the rest of the colours.
Edit: My personal preference for having the flats on one layer is for three reasons:
1. I have a single Multiply layer for all the shading on the characters, and it's easier to create a mask the entire object/character if the flats on a single layer,
2. Fewer layers makes for much smaller files and less confusion,
3. If I need a specific area, I can simply select it, ditto for all areas of a certain colour, which is the same benefit layers have.
Also, just to clarify: I keep my background/environment and character colours (flats and shading) on separate layers, so in reality it's often two layers of flats, not one. The reason for this is to make the best use of the clipping mask, and to allow me to paint my backgrounds a bit without making them unwieldy to work with (painting ruins any selectability the background flats had).