Never boil the lids - just simmer them. Boiling the jars and rings is okay, but the sealing compound on the lids won't work right if you boil them before processing the jars.
With a standard canning jar, I find that the lip at the bottom of the threads is a good stopping point for filling. The height of the ring is about a half inch, which is enough headroom for most canned products.
Make sure you wipe the threads and rim of the jar with a clean, damp cloth before you put on the lid and the ring.
The Ball Blue Book is the standard text for home canning, but it costs money. The USDA guides provided in a previous post are paid for by your tax dollars, a better use of tax money than much of what our government does if you ask me, and are nicely comprehensive.
Don't tap the lids to see if they'll pop down. If the lid doesn't pop down in the middle on its own, then you don't have a good seal, and the jar goes in the fridge for immediate use.
For a boiling water bath, have the water at a simmer when you put in the jars, then bring it up to a boil. You'll have fewer jars break that way. Same as boiling eggs - put in the eggs, then boil the water, so that you get hard boiled eggs insteadof egg soup.
