Actually, matchups are usually the only reason people do have secondaries. If their main could handle everything, secondaries would be unnecessary.
So it really comes down to what you have trouble with as Falco. Falcos tend to have problems with Peach, Samus, Luigi (good ones), and Jiggs/Marth to a certain extent. Sheik and Marth tend to do well against all of those, I'd say that Sheik probably has better matchups against Samus, Luigi, Jiggs, and Marth. So if your Sheik is significantly better, go ahead and use it as your secondary. Just play around with both characters for a bit, see which one you like more.