In answer to your questions. The instruction about the southern bay is very misleading, think instead of the second bit which says "Near the pier".
See note 1 on my picture. Secondly how to anchor? As you say you can see blue balls, yellow, green & red ones. The blue ball is where the anchor is (you can see it when there is no blue ball showing) If you click on the anchor symbol (note 2) you will see a number of choices, the bottom one is another anchor, click on that symbol and the blue ball will show where the anchor is. If you click on the blue ball, when you have brought your ship to a stop, the anchor will be lowered and you can see the cable. Note 3.
As to the largest ship in the game then "Latitude" the VLCC tanker is the biggest in the original basic game, but the Cruise ship "Oceana", which is available as a DLC which you can buy from the shipyard, is the biggest.
http://www.shipsim.com/products/shipyard
Regards,
Angus.