Hello, some gamers only run one flagship, how to combine all the ships in one flagship?

You cannot combine the ships. Possibly other players are choosing not to have other ships in their fleet but this will reduce their strength.

If you are only seeing one ship for other players then you probably have the 'Implicit' mode turned on which will activate automatically if your connection or device can't handle the amount of data for all of the ships on the screen. This will remove the graphics for the other players fleet ships and only show their flagship. The other ships are there though.