Yes they are very well signed. Keisei has a big KEISEI sign on it, and JR is very well marked "JR". There's no way you can confuse the two.

Actually you can buy a ticket all the way through. It's called a "transfer ticket", so you can buy a basefare ticket that covers NRT-Nippori then allows you to go through the transfer gates at Nippori to Shinjuku. You get a separate seat reservation with the Skyliner.

If you didn't purchase the transfer ticket at NRT, you can easily purchase a transfer ticket at the transfer gate at Nippori Station. There's a machine and ticket agents that can help you. Just walk up with your Keisei ticket, say "Shinjuku" to them, and they will give you a ticket that covers to Shinjuku you can use at the JR transfer gates.

There is a JR Yamanote train at Nippori Station every few minutes going to Shinjuku (if you miss one, just wait a few minutes for the next train), I would not worry about missing the connection at Nippori, which should only take a few minutes, and yes it is very well signed to transfer to the JR line.

You might hit some traffic with regular commuters, if you have a ton of luggage I would recommend taking the limousine bus, or later direct NEX instead. If you are traveling light, you can do it ok.