I'm going to make the assumption that you're referring to the original battery R/C 4-6-0 with the plastic drivers and small black controller. If one of your locos is numbered "7" and the second "9," then they already run on different frequencies (27 mHz and 49 mHz respectively) and will run independently of each other. If they're both #7 or #9, then you're not going to run them independently. The same transmitter will control both locos the same.
The most obvious solution would be to replace the R/C in at least one of them with one of the myriad commercial products on the market. It would solve your problem, but quite frankly I wouldn't bother with these particular locomotives. Running them independently isn't so difficult as keeping them running in the first place. The gearing is horrific, noisy, and prone to slipping and stripping. (There's a definite reason Bachmann has gone through 5 distinct drive trains on these locomotives.) The controllers--like many things in the 27mHz range--is prone to interference that launches the loco back and forth suddenly, which only exacerbates the gear problems. The rubber traction tire on the drivers will also stretch and break in short order, leaving you with a rather deep groove in one of the drivers. I'd keep the locos as they are, and let the neighborhood kids run them if they come over. When the locos fall apart, just toss 'em in the recycle bin. (The details are so coarse as to not warrant saving for the scrap box.)
Of course, I say all this while having a 4-6-0 that still operates with the original drive train. It's usual job was as a helper on the steep 6% grade on my dad's railroad. I did replace the wheels with metal ones, and have collected the gears from other defunct 4-6-0s to keep this one running, so with a bit of work and the proper care, they can be made to run halfway decently. (It actually hasn't run in quite some time, as the diesels now handle the helper district.)
This probably isn't the answer you were hoping to get, but in terms of operational success stories, this locomotive was decidedly not a shining example. The current version, called the "Anniversary" or "Annie" is far, far superior in every respect, and can usually be found for around $150. It's not R/C, so you'll have the cost of adding that, but you'll end up with a locomotive that can run independently of the other, and--more importantly--run in the first place.
Later,
K