What does this mean? there as we ran in we saw the squadron waiting, the trim ships drawn up side by side, and all our troubled friends who waited, looking seaward. we beached her, grinding keel in the soft sand, and waded in, ourselves, on the sandy beach.

I'm not sure but I think this is what it means:

When [we] ran in, [we] saw the squadron waiting. This means they ran in wherever they were running in and saw a group of military soldiers that were lined up in a military formation, called a squadron. They saw their friends waiting for them, troubled, looking out at the sea. They beached, or laid the ship (her) ashore and grounded her/the ship to shallow water in the sand. Then they got of the ship and waded through the water onto the sandy beach.

I hope I helped! Again I'm not sure if I am correct but I hope I helped you somewhat.