You assign the ground seed to the pin on the part if you want it connected to the ground fill - right-click on pin -.
The ground pins only light when there is no ground fill, so you test it throughly before and then ground fill, but even after ground fill there should be a ratsnest dotted line still connecting grounds.
Pin ends only change from red to green when there is a physical connection.
You can link islands with links, or organise it so they can connect, or use one side of a double-sided board, or use a physical trace - red blob to red blob on the islands -, or you can set the ground fill keepout smaller so that it might be able to snake a connection, or use a via to the other side ground fill and then another via back to the other island.
You can upload it here - 7th button - and someone can look at it.