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Can we get a little more information, such as your team (Pokemon, levels, moves, etc.), the items you have, etc.? That would make it a little easier for us to give advice on how to beat the gym. Thanks.
First and foremost, I would look into adding three more members to your team. Even if you won't use them, they'll be useful as sacrifices to take hits you don't want your main battlers to take or to switch into to revive or heal one of your main battlers safely. I would definitely considering getting a Geodude and evolving it into a Graveler at level 25 because it will make your life much easier in this fight. Geodude can be found on Routes 111 and 114, Victory Road, Safari Zone (Rock Smash) and Granite Cave (walking and Rock Smash). I believe Granite Cave is the only option available to you at this point, but I could be wrong as its been a long time since I've played a game in Hoenn. Nincada might also be a good option due to its Ground typing, as long as you don't evolve it (granted Shedinja would be helpful for the most part in this fight as long as it isn't confused). Second, I would level up your Pokemon to give you a bit more of an advantage, probably to around levels 25-26, especially Shroomish as it evolves really close at level 23 into Breloom. Third, I would stock up on Paralyze Heals as the paralysis from Magnemite's and Magneton's Thunder Wave can be quite difficult to deal with.
As for actually dealing with Wattson's Pokemon...
Combusken's your best bet against the Magnemite and Magneton if it knows Ember and Double Kick. I would probably use it straight out of the gate to take out the Magnemite (he does start with Magnemite, right?). Shroomish/Breloom might be nice to switch into if Combusken is in danger as it resists Electric type attacks and, if it is a Breloom, can also dish our super-effective Fighting type attacks on Magnemite and Magneton. Gyarados isn't really going to be much help here unfortunately.
If you hold down the B button when a Pokémon is evolving, it will cancel its evolution, though not permanently. So you could level up Nincada but after level 20 you’d have to prevent it from evolving every time it levels up.
I definitely wouldn't stop it from evolving, that Shedinja is more than worth it and can solo 2 of the 3, though that's complicated by confusion of course. However I think there's a lot of overkill here regardless. Level up Shroomish to 23 and get Breloom, who would guaranteed 1 hit KO Magnemite, and guaranteed 2 hit KO Magneton and Voltorb. Meanwhile outside of Self Destruct the best they can do you is a 4 hit KO, and even Self Destruct won't kill you if you're above 70% health. Bring 4 super potions and 2 revives and you are virtually guaranteed to win, even with the most obscene confusion luck possible.
Alternately, you could get that Geodude to level 20, and Magnitude has a 95% chance of OHKOing the Magnemite, a 50% chance of OHKOing the Magnetude, and is a guaranteed 2 hit ko on Voltorb, even with garbage IVs and no EVs. Meanwhile the strongest move they have vs him does guaranteed 3 hit KO. He at that point could also solo the battle, and combined with Breloom it'd be laughably easy. You might eventually want to get it to 25 and evolve it into Graveler, which is a good pokemon which can put in some solid work, especially if you have the ability to evolve it into a Golem. However it's not even remotely necessary to turn this fight into a breeze, nor is leveling the rest of your Pokemon or any of that. I suspect it'll be easier to get the Shroomish to 23 than to get the Geodude to 20, or any of the rest of it, but regardless of what you choose, my point is that I'd do ONE of those things, not all of the things recommended.