I am going to install a 13kw generac, it comes with a 100 amp transfer switch. I am going to upgrade to a 200amp transfer switch so I can feed the entire panel. The site has two choices, RTS-N and RTS-E. How do I choose between the two?

I believe N is for indoor use and the E is for outdoor use. You might give a call to Generac company to confirm.

When I called Generac they said to "consult with my electrician"...

If that is the case I would call a supplier that is going to sell you're the switch. As the supplier that is going to sell you the switch they will have to give you a answer before they take your money. LOL

I can tell you this much. Do not use a back door supplier on the net because you will probably not get any type of service if you need it. I might pay a bit more for my electrical supplies but my vendor always has been helpful on warranty etc.

I would like to mention that the Generac Company has alays answered my questions on there products by phone. I guess you got a person who did not care that day about answering questions.