Open the header tab in Advance Map and then change it to 'Professional Header View' (Ctrl + H). At the bottom of the map data section there should be two windows where you can define the height and width of your border blocks.
The green script tile which is blocking Cinnabar Island Gym needs to go through several steps before it is deactivated for good. Firstly, when you pick up the key in Cinnabar Mansion you will automatically set the flag 0x1A8 as that the event's Person ID in the overworld. Secondly, when you enter the main Cinnabar Island map, a level script will branch off if flag 0x1A8 is set. I've copy pasted the important parts below.
Code:
#org 0x166EE1
setworldmapflag 0x898
call 0x8166F5E
...
#org 0x166F5E
checkflag 0x1A8
if 0x1 goto 0x8166F68
return
#org 0x166F68
setvar 0x4001 0x1
return
As you can see, if the player has set the flag 0x1A8 the script will branch off to the command 'setvar 0x4001 0x1' before returning to the main body of the level script. Ultimately it is this setvar command which deactivates the green script tile in front of the Gym. This is because the script tile's variable number is 0x4000 and its value is set to 0x0, which means that the script will only activate if variable 0x4000 has the value of 0x0. Since the level script will always change 0x4000's value to 0x1 once you take the key, the green script tile won't activate anymore and the player will be able to enter the gym freely.