It is not too complicated if you follow the directions, eg ride one train, then make the connection to the line as indicated. This is Japan, so you you might have to make connections to other places.
However if you wish to go to Tokyo tower from Shinjuku, you have a few ways, the easy way: Get on at JR Shinuku Station, take the YAMANOTE LINE to HAMATSUCHO Station (at Shinjuku Station, board Yamanote Line trains that are going in the direction of "Shibuya, Shinagawa", the trip should take about 25 minutes. At Hamamatsucho station take the NORTH EXIT. If I recall correctly the walk was about 15 or so minutes to the tower.
More assistance on using trains in Tokyo: tokyosubway.info