I'll second DFix's book suggestion. It's a good reference on knot tying that is easy to understand.
As far as loops go I am a proponent of their use. This is mostly due to having broken off 1/2 a wisdom tooth when I was stupid enough to hold the tag end of a leader in my mouth while I tightened a nail knot.
The loops should be small, about 1/2 inch in length. For the fly line I use the whipped loops in the Lefty Kreh/ Mark Sossin book rather than the Cortland loops that are sold in shops. My experience with the Cortland loops is that eventually they slip and at best you have a hinge in between your line & leade. At worst you have no leader, fly and fish. On the leader I use a small perfection loop.