Hot pack them, using the directions for crushed tomatoes. You don't have to process as long, either, for the hot packed tomatoes.
Raw packed will float more. They are fine as long as you added the necessary bottled lemon juice/or citric acid and pressure canned them for 25 min., 11 lb. dial gauge, 10 lb. weighted gauge, unless you needed to adjust pressure for higher altitude.
How to can crushed tomatoes.

Here is a link that might be useful: Crushed tomatoes.

When you peel them, place them in a large colendar to allow some of the water to leak out. Also lightly sprinkle the layers with a little pickling salt. Because they are whole, and contain a lot of captivated water as well as seeds, you always going to have this water leak out and settle to the bottom of the jars. Using a very dry plu tomato may help. I have grown some that have a very small amout of water inside, and are much more meatier. Adding tomato paste or a thick sauce to each jar to fill it, can also help. My last batch of whole tomatoes was so thick, it was almost the consistancy of ketchup. I do add citric acid to mine, so that they can be BWB canned. When you serve them, pour the jar into a colendar and allow the water to run out first.

Your suggestions are great, thank you! I'll try both approaches. Do you have any opinion about the seeds remaining? Do they end up being bitter so that they need to be taken out when you actually use them? I cook tomatoes for sauce with the seeds in and they taste fine, but I simmer it for an hour or more. Any ideas about this?

Canned tomatoes aren't normally seeded. Tomato sauce often is.

It's purely personal preference. Some people taste the bitter but others aren't bothered. If you're not bothered, leave them in.

Carol

In high concentrations, the seeds can be bitter. I used them along with skins and cooked it down to a thick past, only to find that it wasn't very tasty. Seeds in a tomato product is OK, unless you like a sauce that has no seeds in it.