Well now you have the first password, the second one requires a longer procedure. What you need is on Six Island.
On Six Island, make your way to the Dotted Hole. Look at the message on the door. It's written in Braille, the language of the blind. Use Cut on the door to open it. Once inside, there's more Braille on tablets in the center of the room. There are also holes on all the the walls in the room. The tablets tell you which holes to go in, but I forget what the order is. Here's a hint so you can figure it out though. If you have to take the top hole, the message is only two letters (which spell "up") and if you have to take the right hole, there are five letters (which spell "right"). Left and down both have four letters, but here's how to tell them apart. Each Braille letter is made up of six dots. The first letter in "left" has the three dots on the left side filled in while the three on the right side are blank. So, if it's four letters long and all three dots on the left side of the first letter are filled in, go left.
When you finally reach the bottom, a scientist will take the Sapphire from you, but he'll give you the other password for Team Rocket's base. Go back to the base and beat all the Team Rocket members there. Once you're done with them, you can battle the scientist that took the Sapphire from you. Beat him and you'll get it back. Give it to Celio and you'll be able to trade with R/S and Colosseum.
~Kipper~