yeah, the frequency system tracks specific landmarks within approximately 500m of the player's current location. higher percentage means you are closer to the landmark in question
the game has a total of three areas from A to C. in each area exists a door to the main tower that will not open until you find and successfully chain all 5 sub towers in an area without running out of time. once done, enter the main door, shoot the big tower, and proceed to the next area
in addition, there are various upgrades scattered about that you'll need to progress, eg: some doors only open when you shoot them with a specific weapon
hope this helps!
edit: oh, yeah; some upgrades are tied to specific areas. if you didn't get any results, try tracking in a different area