I have some general questions about the silk patterns, these are probably questions well know to others but I'm new at PCB software, so here goes.

Picture "pattern1.gif" shows a silk pattern for an Electrolytic cap, "pattern2.gif" does also, my first question is: is it ok to have screening on top of a pad like pattern1.gif, or should pads have clearance as in pattern2.gif"?

My next question is, how and why do some patterns have partial green and partial gray as seen in picture "pattern3.gif"?

Pattern1.gif shows what you shouldn't do. Pads should be free from silkscreen, otherwise you won't be able to solder them.
Green lines are silkscreen, by default. One arc was divided on 4 small arcs to avoid overlapping pads. Grey lines are assy layer. They are not populated on a board, therefore they can overlap pads.

Ok thanks for the info Alex.

BTW, is there any ebooks or other reference material I can look at/for about what's right and what's wrong doing PCB files for use with PCB manufacturing houses? As you can well perceive I'm new to this and have no experience with PCB file etiquette.

I've had people say to me "check with your board house" but that is like having the "cart before the horse" seems like I must make files _first_ then shop for a maker.

A quick search yielded these:
http://www.alternatezone.com/electronic ... alRevA.pdf
http://www.selectcircuits.com/index.php ... n-tutorial
and others.