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There are some major ones in fixed positions, and the maps in the GM's guide show those. But basically they just show up as the plot needs. The old Rifts main book had a chart to determine the length of a randomly found ley line but it's pretty much GM fiat as to where they may be.

I just make sure I mark these on my home map so that when they return to the same area, I do not make a mistake about where it is located.

Geographic location makes a big difference in how often you run across ley lines. If you're in the Magic Zone or England, for example, sometimes you can't stop to take a leak without stumbling over a ley line, but in places like the New West, they're rare enough that you might never see one.

That being said, you can always put them wherever you need them to be for your purposes.

Any time a player says "I'm looking for lines" I always let him find one close.
Now that I think about it, I have NEVER given players a random line encounter. Weird. Thats like a huge part of Rifts Earth.

Not normally. I have that one map in the book with all the Nexii, but I dont keep track of every line. If a mage wants one I let him have it. If he needs a nexus I make him search a bit, and theres almost always someone or something else there. Good for a random encounter.

As frequently as the story needs them.