What is more natural for you to say this:
Yesterday, [via / through / on] website I talked to my friend named Johnny.
Yesterday, I talked to my friend named Johnny [via / through / on] website.
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It depends on the context and the situation. Most of the time, I would find this one more natural:
Yesterday, I talked to my friend Johnny using Skype.
However, it depends on what I'm trying to emphasize. If I had never used Skype before yesterday, and I'm excited about this new tool I can use to talk with my friends, I might say:
Yesterday, I used Skype to talk with my friend Johnny.
because the main thing I'm trying to stress is the tool I used, not the person I spoke with. (In the first sentence, I'm putting more emphasis on who I conversed with, not the tool I used to communicate.)
Funny, though: when I'm talking about a letter I receive in the mail, I almost always put the person it was from at the end:
Yesterday, I got a letter from my friend Johnny.
Yesterday, my friend Johnny sent me a letter.
That's because, if I got the letter yesterday, chances are Johnny sent it a few days ago, not yesterday. However:
Yesterday, my friend Johnny handed me a note.
is perfectly fine, because the transaction is instantaneous. I would not say:
Yesterday, I was handed a note by my friend Johnny.
because that is in the passive voice.
Notice also that I have removed the word named. When talking about my friend Johnny, the word named is usually omitted.