Seedot and Makuhita are found in the 'Sandy Desert'. They are fighting until they notice you. They then come after you. You have the option to dodge one of them. The one you dodge falls and runs. You are left to fight the other. If recruited, Seedot will make a café on the island. If recruited, Makuhita will make a fighting Dojo on the island.
After the 'Rock' storyline is finished, you can revisit this area and find the other which escaped.
Ralts is found at the bottom of the hidden temple in 'Sandy Desert'. It doesn't notice you until you approach it. It then attacks, you only have one chance to recruit it. If recruited, it will work at the 'Itemfinder'. It tells you the location of items in any map.
Gardevoir is found at the bottom of the hidden temple in 'Sandy Desert'. It will only appear if you recruited the Ralts and have finished the 'Woodland' storyline. It will try to launch psybeams at you and you will have to make it through the maze to find it at the end, if you get hit, you lose HP.
It will be recruited if you beat it in a battle after finding it. If recruited, it will upgrade the 'Itemfinder' and make more maps available for itemfinding.
Regirock is found in the 'Dry Desert', which is only available after the 'Rock' storyline.
It is awakened by your presense. If recruited, it will sleep in the 'Heated Cave' in the Mountain Cave.
Regice is found on the 'Cliff', which is only available after the 'Rock' storyline.
It is awakened by your presence. If recruited, it will sleep in the 'Frozen Cave' in the Mountain Cave.
Registeel is found in the 'Abandoned Mansion', which is only available after the 'Rock' storyline.
It is awakened by your presense. If recruited, it will sleep in the 'Hard-Rock Cave' in the Mountain Cave.
Regigigas can only be found if you have recruited Registeel, Regice and Regirock. The trio will be found at the newly opened 'Mixed Cave'. Registeel, Regice and Regirock will be walking in circles around a statue and then the statue will be awakened. Regigigas walks throught the wall. It then stays at your town, holding events and giving prizes on certain days. He is thankful for you rescuing him from he's 1001 year slumber.