1. Do you know if Legal Zoom is legitimate?
I have never personally used it, but I think it is legitimate.
2. One question is "who should be listed as a contact for the IRS to contact if they have questions on my LLC application or EIN #. I want to remain anonymous from the LLC so how can I provide this?
If you don't want to put your name, you would have to list another member or your accountant/bookkeeper.
3. How should I manage taxes and employees as a pass through entity or corporation?
LLC's provide for pass through taxation, which will allow the member/s to pay taxes on the business profits on their personal returns. This is usually better than to have the taxes paid through the corporation - - if you were to set up a corporation (inc.).
4. Who will the representative be that is registered with the state for PA sls tax? Again how can I avoid this as an anonymous owner?
If you don't want to use yourself, it would have to be another member or an authorized agent that you hire - - like a lawyer or cpa
5. Legal Zoom provides something called Registered agent. They said this protects my anonymity. Is this true?
Sort of. A registered agent is required by law, and this is the person who can be served with legal process/summons in the event that the LLC is sued. This can be an attorney, a member of the company, a corporation, etc.