The hourglass spots were simply intended as a visual aid to the player, letting them know how long their meeple will be tied up at that Location in order to progress the Progress Track one step. In hindsight, they could have been designed to look less like "spots you place a meeple on."
E.g. the Poison Traps requires two turns. You visit on your first turn and go to spot 1. During #6 Resolve Locations, you would advance to the Build Spot. During the next turn, you essentially skip Phase 1 (Goblin Keep) since you're at the Poison Traps. At #6 Resolve Locations on your second turn, since you are in the Build Spot (and assuming there are no Invaders present), you would return your meeple to the Goblin Keep and advance the Poison Traps Progress Tracker one step.
E.g. the armory and forge Locations are simpler. If you visit there on your first turn, you will advance the progress tracker 1 step (actually, 1 step for each player there). As an aside (and as is mentioned in the Rulebook), Invaders prevent Locations from being Resolved, and Backstabbers count as Invaders. So, if a player backstabbed at, say, the Armory Location and was not defeated, then no progress can be made on that Location's Progress Tracker.