The station map (of Shinjuku Sta. of JR-East) seems to be based on this one.
http://www.jreast.co.jp/e/stations/img/map_e/e866.pdf
The right on the station map is about the north in reality, while the right on the Odakyu's map is about the east. : how I get to the Odakyu desk. I will arrive with the Metro (Shinjuku-Line from Motoyawata).
Shinjuku Sta. of Toei subway: Solid map (in Japanese)
http://www.kotsu.metro.tokyo.jp/subway/stations/shinjuk...
Toei Shinjuku Line's Shinjuku Sta. platform is on the 5th basement (B5F). You can reach the 1st basement (B1F) by an elevator.
Presumably (sorry if that's not correct), the exit numbered 3 leads to underground shopping malls, Keio Mall and Odakyu Ace (south block). Around the corner of Odakyu Ace (south block), there will be someone who tells you the stair leading to Odakyu Department Store if you ask where Odakyu Honkan (= main building) is.
By the way, will you come straight from Motoyawata to Shinjuku? If so, you can choose a JR train for Nakano or Mitaka leaving from Track 1. The train will arrive at Track 15 & 16 platform in Shinjuku Sta. of JR-East, which is closer to Odakyu Department Store than Toei Shinjuku Line's platform. The required times for rides are about the same, both around 40 minutes.
As to "Metro":
Not "Metro" but "Toei subway" is used for 4 Tokyo subway lines whose names begin with "Toei." They are operated by Tokyo's Bureau of Transportation.
"Metro" is used for 9 Tokyo subway lines operated by another operator Tokyo Metro.
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