The second Tower is just a little bit North from the first one, on an island. Before you enter Tower 2, go back to Crysta and buy an Ice Ring from the MagiRock shop. You'll need it for the last floor of the Tower.
You will have to go up both sets of stairs, but I recommend going up the right one first. Ark will be on the second floor, where there is a switch to the left and a MagiRock at the south end. Once you flip the red swich, go back down the stairs to the first floor, and then go up the left stairs.
This is the main second floor area. There is a new monster, besides the purple pill-bugs and the firewheels, that looks like a wizard. He can "look" at you and temporarily make it so you cant move. But he only has 20HP. If you go south from the staircase you arrived on the second floor with, you'll find a SBulb. To the right of the staircase there is another red swich. Flip the switch and the doorway near the top/center of the room will open.
The third floor looks like a giant donut. There is a red switch in each of the 4 corners of the room. All 4 swiches need to be flipped in order for the entrance to the next lever to appear in the middle of the room. Dont forget you can move the statues that have pink jewels on their foreheads!
The fifth floor is another donut-shaped room. But there is a barrier in the way to get to the center of the room. Directly to the south there is a red switch that needs to be flipped and unfortunatly it is across a gap in the floor. Equip the Jewel Box as your item, face the switch, then press the X button. You will get a menu above your head and you can choose which ring you want to use by pressing the directional buttons, and then pressing B to confirm. If you choose the Ice Ring, an icicle will fly from your hand and if you're pointing the right direction, will flip the red switch and drop the barrier in your way.