First off, and maybe I am wrong. You need a certian type of ship to move troops across water. I made longboats and couldnt move across, I read the book 5 times and was getting really frustrated. Then I tried making the other type of boat, and lo I could move my troops across water. So I figure longboats are for taking/holding a water region and the other boats are for troop transport.

One tip, if you send your army to take over a territory that does not have a port, or if the port is destroyed during the invasion then you troops are STUCK there. So dont send any troops thinking you can get them home if you need them.

As for yellow, when trying to move across land you can move a troop thats more than one province away. When you hold it over the province its yellow to let you know that it will take more than one turn to arrive there.