I tune my electric guitar using a tuner on my iPhone. When I'm tuning my guitar, should I use the sound come from an amplifier or the sound of the guitar itself?
Granted that your amplifier isn't terrible, it should be fine through the amplifier. What's more important is any possible sound effects that you have on it. Things like distortion and vibrato can cause difficulties for a guitar tuner to pick up the string's actual tone. This is why tuner pedals are usually the first pedal in the chain, too -- the tuner only cares for the sound's pitch, so it's best to leave it unmodified.
I do think that using an amp when tuning with an iPhone is useful though. I can imagine that your guitar will sound too quiet for your iPhone to pick it up when you don't amplify it.
If you have a guitar input for your iPhone, which your tuner app supports, then plug directly into that.
If your tuner app has to use the microphone, then plug your guitar into an amp, so the microphone has something loud enough to hear. Get as clean a sound as you can, for tuning.
Tuning via a microphone is problematic in noisy environments -- for example, busking on a busy street, while people are chatting in a dressing room, while the rest of the band is noodling.
If tuning with an app becomes a hassle, consider spending US$20 or less on a dedicated tuner. Or, most multi-FX pedals have a tuner built in.
Tuners with only a jack input are only suitable for electric and electric-acoustic guitars.
Clip-on tuners, which pick up vibrations from the headstock of the guitar, work well on acoustic guitars, and acceptably on many electrics.
Are you plugging directly into the iPhone or are you attempting to have the iPhone's microphone pick up your guitar? It's best to eliminate the most extraneous noise possible. Using an amplifier can cause inconsistencies as you are relying on the phone's small microphone instead of a direct signal.
Advice: purchase a pedal tuner or a digital Korg instrument tuner - they are indestructable and you can plug directly in to them.
I would recommend you to buy a real hardware tuner. In which you can plug directly your guitar for the best tuning.
Thus, iPhone microphone might not catch the exact frequence, iPhone was not designed specificaly to tune guitar. So your tuning might be approximative.
But IF, I mean IF you still want to tune your guitar with your iPhone, I recommend you to use your amp with, of course, clean sound. To be sure that the iPhone catches the sound.