The way I had figured it was I wanted to have 3500 AP MINIMUM before worrying too much about armor pen. This way I had a decent stable stat. As of right now I have nothing BUT amor pen gems aside from a few hit ones - get yourself a grim toll (this will prove very useful later on) so you can replace all hit gems and when you start getting more current gear the AP will come natrually.
To this day I only have 3800 AP, but I have nearly 80% armor pen without grim toll. Start gemming for armor pen, you won't regret it.