Running a Cat5 directly into a phone(Newbie)

The standard method is to wire the first line (red/green) to the white/blue pair and the second line, if any, to the white/orange pair.

The pairs are the two inside and the two straddling them on the outside.

An RJ11 plug can accomodate two lines; one on the red/green pair and the other on the yellow/black. When using CAT5 cable these are commonly installed using the blue/white-blue and orange/white-orange wires. The remaining green and brown are unused; it's common to coil them back around the insulation rather than just cutting them off.

So yes, a single line would require only two wires. But it's a good practice to connect all four wires for both pair in case you ever need to add another line in the future. If you've got the wire, why not? It'd sure save you the pain in the ass hassles of opening the box later just to attach the wires!

Black Box has several pages on color codes and good practices for wiring communication equipment. I suggest that you get one of their catalogs.