When you beat a tower or dungeon, it is explicitly stated where you need to go. This is so, because people got too lost while playing BB/SB.
So, you beaten the first tower? Then you either beat Witch Warcastle in town, or go to the northeast corner of the main overworld, into the cave, then up to the east of Mt.Death where the next tower is close by. Pay attention to get the hookshot upgrades. Each upgrade is available 1-2 dungeons before you actually need it. Plus be on a lookout for sword and defense upgrades. If you can access the main overworld, you already can get at least one of them. Be sure to memorize what item triggers what specifically in GM.