I’ve seen many players in 1650 and Fourth Age sail to an enemy target, attack the target and move inwards, leaving their ships beached on the coast of the captured popcenter, usually never to be used again. This is such a waste! Those ships could be used for a second invasion in a few turns, and the warships could be used for defense of your coast!
The best way to handle this is to arrive with two navies – the second navy should just have 1 transport and if necessary, a couple of warships, and plenty of food. The large invasion force attacks and moves forward, and since the attack has beached the ships, the second navy simply picks up all the ships and sails out.
Another way is to have your commander be a champion. I’ve done this as the Corsairs, with Teldumeier. He captures the popcenter, splits off 100 troops to a subcommander, and marches forward. The subcommander, now in charge of his own army, picks up the ships and sails off.
A third way, if you are making landfall where there is no popcenter, is to simply split off the bulk of the troops to a subcommander who marches to a target, while the navy commander sails home; or if you are at a target, the navy commander captures and then splits off most of the troops to a subcommander who marches off. Next turn the navy commander with his few troops, picks up the ships and sails off. This only works if you can be reasonably sure how many troops to split and still retain at least 100 troops! If you are planning ahead, you might want to ensure you have some number of a second kind of troops to facilitate this – say, 400 LI and 2100 HI on 10 transports, that makes it easier
Ships are too valuable to simply be beached in a foreign land!