I have 2 separate jacks for 2 lines, Line 1 is Primary and Line 2 is the second line. I want to make Line 2 as my Primary meaning switch those 2 lines, how can I do that?

It actually depends on how things are wired.

Here is a good reference: Doing your own telephone wiring (http://www.ling.upenn.edu/~kurisuto/phone_wiring.html)

You basically switch T1, T2 and R1, R2

Green/Red is the typical line 1 or the G and Y terminals.

But it depends on how things are wired and where.
Some examples:
1) The wiring could be changed at the NID
2) Both lines run through the same cable, but are just interchanged at the jack

One of the better ways of doing this is to make the wiring standard red/green and yel/blk for line 1 and line 2 and to switch using an adapter that's plugged into the wall. The adapter has 3 jacks (L1+L2, L1, L2). The first would be used for a 2-line phone, line 1 to a std phone and L2 for line 2 to a standard phone.