We use the system where player 1 picks an area to keep, player 2 picks an adjacent area, etc. until we have the right number of areas. I'm nearly positive this is how the designer, Friedemann Friese, taught us. If not then we picked it up from the earlier version of the game, the crayon-based Funkenschlag.
One tip: when the new (current) edition came out I had a chance to play with the designer explaining the rules. We used the pick-an-adjacent-area rule to pick our staring zones and were using the Germany map. With six players we picked five zones, and the one left out was the center zone, leaving a ring-shaped map. Friedemann immediately exclaimed, "We never playtested it that way!"
It turns out that's a pretty poor map to play on since you're restricted to expanding through other people's territory much earlier in the game than you normally would. The result was an extra-long game that frankly wasn't as fun.
So the tip: if you play the Germany map with 6 players, do not eliminate the center territory.