Hey Gubar it's an almost impossible question to answer. It needs a book or two, the tutorials you're reading, and a LOT of hands-on. I spent all my free time last month on the challenge and I still not got a command of UV'ing. See if you can pickup Michael McKinley's book The Game Artist Guide to Maya. I've ordered this one but it's not arrived yet.
1. It really depends on what you are mapping. Automap is great for non-organic objects. Automap is fine as a starting point for organic meshes too. The advantage is that it keeps the scale correct for the shells. The disadvantage is that is produces a bucketload of shells and much manual labour is needed to stitch everything up and avoid stretching. There are other methods for organics that work well too (cylindrical map for half a head comes to mind). ABF and LCSM are two algorithms for UV'ing on the move. I think it originates from the blender developers research (I might be wrong on this one) and you'll have to do some reading up on the subject.
Anyway here's more info and a nifty plugin called Roadkill: http://www.pullin-shapes.co.uk/
Usually auto anything is not so good for CG, and no matter what you use you'll have to do manual labour. So you will have to do a ton of testing and trying out things to arrive at a workflow that suits you.
2. You can have as many shells as you want within 0-1 space (the upper right quadrant in the UV editor). UV space can be shared with overlapping. Again too broad a topic for a forum post. Also I hear having as few shells as possible is better, but I am not exactly sure why. One aspect is for texture painting in other application like Bodypaint or Zbrush, but Zbrush handles all kinds of UV layouts. I simply don't have sufficient info on the matter.
Another aspect is the seams you mentioned. You want to have as few seems as possible to cover up come paint time.
For sharing texture space there is also a lot of trickery that can be used:
3. Yes they do differ in how they project the texture onto the object. More reading is required.
You can use any projection you want for one area of a model, and a completely different projection method for another area and so forth.
Don't take my answers here as the ultimate guide to UV'ing in any way. These are just some thoughts on the matter and not anywhere near in-depth enough. Simply too broad a topic.