To get the Ecruteak Gym Leader Out, you must fight your rival in the burned tower in the upper left corner of the town. After you're done, a hole will open in the floor, and you'll fall down. Move up, and you'll see the three legendary dogs (i.e. Suicune, Entei, Raikou), and all dogs will run away except for Suicune which will come near you and then run away. When they're done, move down and you'll meet Eusine. After he blabs about you ..., he'll go away. Just move down again 'till you see a ladder. Go up on it and you'll end up at the entrance of the tower. Go out, and go to the gym (after you heal your PKMN ofcourse , and train them real hard 'cause all trainers inside that Gym have only GHOST type PKMN). To go to Cianwood, you must fight the Kimono girls in a small house in Ecruteak (near the PKMN center, up a bit). Fight them all (as a suggestion, fight them before fighting the Gym Leader 'cause their PKMN give a lot of EXP.). When you're done, in the same house, talk to a man wearing a hat, and he'll give you HM03 (SURF). When you're done from Ecruteak's Gym, go to Olivine and enter a small house (a sort of cafeteria) and talk to a sailor sitting down and he'll give you HM04 (STRENGTH). Teach SURF to a PKMN and surf down from Olivine's shore. There are a lot of trainers there, so I suggest you fight them all as training for you. When you're done, you'll reach an island, Cianwood. Fight its Gym Trainers. Teach STRENGTH to a PKMN, and move the boulders in the Gym to encounter the Gym Leader. Use FLYING and PSYCHIC PKMN to defeat his FIGHTING-types. When you're done, step out of the Gym and talk to a woman infront of the Gym and she'll give you HM02 (FLY). Go down the last house in Cianwood and talk to its owner and he'll give you the cure for the girl's PKMN in the lighthouse. Teach FLY to a PKMN, or just SURF back. Go up again the lighthouse and give the cure to the girl. When she's done, she'll head back to her Gym. Follow her and train your PKMN hard 'cause she's got STEEL type PKMN (better have a WATER and FIRE PKMN).
In case you're stuck anywhere, just tell me, and I'll be glad to help you out.