You have to dive next to the rocks and re-surface on the other side. No worries :)
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In order to get to Paciifilog in Pokemon: Emerald, you must start in Lilycove and go around the waves. Starting at Lilycove, surf Route 124 until you get to the house on the water. Turn right and surf down Routes 127, 128, and then 129. On Route 129, take a left to get on Route 131. Keep heading west and you will see Pacifilog.
KYOGRE is in marine cave which is on route 105, 125, 127 or 129 depending on the weather but it will only appear once you have defeated the elite four
Dive near route 127 near Mosdeep city then go inside the cave where the submarine of Capt. Stern then dive back up
on route 127
The eighth gym is in Sootopolis city which is near route 126 and 127 (you have to dive to get there). First you have to find Wallace in the Cave of Origins in Sootopolis city and tell him that you think Rayquaza is in the Sky Pillar. Then you have to find the Sky Pillar (route 131 through a space in the rocks) and battle Rayquaza. It will then fly away. You then go back to Sootopolis city where Rayquaza will stop Kyogre and Groudon fighting. Then you can go to the gym there(: