How to use metro from Haneda to Shinjuku?

Going to Japan in a few days. Landing at Haneda airport. I'm a bit confused by the metro system. Google maps tells me that to get to Shinjuku, I have to take the Keikyu-Kuko line to Shinagawa Station and then the JR Yamanote line to Shinjuku Station. Does this mean I have to buy two tickets for each line, or will I be able to purchase one ticket that works for both?

Do yourself a favour and take a limo bus. Contrary to a common misconception, access to/from Haneda by rail is usually a pain.

http://www.limousinebus.co.jp/en/

Can�Lt really say that Haneda connection by rail is unpleasant. Other means of transportation are usually slower or much more expensive. I would buy a Suica card and charge it with some yen and then dont worry about buying tickets.

Buy PASMO(IC card ticket) at Keikyu ticket vending machine, just touching at ticket gates.
http://www.pasmo.co.jp/en/

In Japan, urban city railways/subways are not called "metro".
In Tokyo "Tokyo Metro" is one of Subway(underground) rail company name, another one is "Toei".
https://en.wikipedia.org/wiki/Transport_in_Greater_Tokyo
So, JR and Keikyu are not "subway". (ground rail track companies)
PASMO covered most railways and buses as one card, but no discounted card.
Jump to Keikyu or Tokyo Mono rail web fr HND(int'l) web and see the discounted tickets info.
(Have you ever imagined how many trains are operating in Tokyo?)
http://www.demap.info/tetsudonow/

Limo bus easiest right, if in weekday morning(around 7:30 - 9:00)
and evening rush(around 16:30 - 19:00) or heavy luggages with.

If not solo, fixed rate taxi also may good.
(need booking, EN online booking form provided)

Having to navigate urban commuter rail, with luggage and tired/jetlagged from the flight, and when you're not familiar with it, as OP obviously isn't?

Signs are plentyful and in english. Station staff are numerous and helpful. I don�Lt consider it so hard.

But the OP can of course decide for himself how complicated he views the situation.

Actually what you found on the internet is exactly the right information.
I wouldn't say that the connection is difficult, just one change of train. But this obviously depends on your personal skill with public transport.
As previous posters said, if you take Keikyu and Yamanote line, it is advisable to buy a Pasmo/Suica card. You will use it every day while moving through Japan.

Obviously taxi is easier but more expensive.
I personally find bus quite slow, but it is perfect if there is a bus that stops right at your hotel. It's also more expensive than by rail.

Enjoy your travel to Japan!

If you're staying for a while you're best off with a Suica card or similar; it won't save you any money but is definitely easier to get around.

I always wonder what you mean by the metro system.
In Tokyo, the word "metro" means the two subway companies, or in particular one subway company whose name is "Tokyo metro", not the urban train system in general.
See first this page and have a general idea of the Tokyo train system.
http://www.japan-guide.com/e/e2017.html

You have in Tokyo three categories of the train companies: the JR East, the subway companies and the private railway companies, and each company has their own line(s). Don't mix up the companies and the lines. They are closely connceted for your convenience, but they are different companies. Therefore, you pay separately for each company. But it doesn't necessarily mean that you always have to buy separately tickets each time. You can buy through tickets, in almost all cases, or you can adjust your additional fare at your station.

At least in Europe the word 'metro' is commonly used for the means of transport referred to as 'underground' or 'subway' elsewhere and does not need to refer to the operator. Even in UK English you see it pop up every now and then, or maybe that is just in London. :-)
Short for Metropolitan as the Paris Metro is officially called.

Thanks, guys. I'm probably going to get a PASMO card since it sounds like it would be useful and more effective in the long run. I'm hoping that the maps and line changes aren't too confusing. Shouldn't be too hard (based on the responses).

There are some stations of different names in and near Shinjuku.
Is Shinjuku Station of JR actually close to your first destination?

In Shinagawa Station(s), there is a Keikyu-JR transfer gate, which works both as a Keikyu exit gate and as a JR entrance gate.

- JR-East: Shinagawa Station
https://www.jreast.co.jp/e/stations/e788.html
: You see "Keikyu Line Transfer Gate" around the top of the map.