My chowders usually consist of a fish fumet with the addition of clams.
If I don't have the time to prepare the fish stock, a standard mirepoix (carrots, celery, onion) & bouquet garni (parsley/thyme/bay leaves) should work too for a soup base.
One of the easiest & best ways to make a soup thicker is to add a few EXTRA potatoes (diced) to the recipe you're using. Or add some non traditional chowder veggies like zucchini & yellow summer squash.
For cream type soups, roux is typically what you would use as thickener @ the last minute.
Also if you want more complexity to your soup, pan roast all your ingredients before you add water.
Since you mentioned the bacon is NOT noticeable, SAVE it for the end as a topping/garnish when you're about to serve. Brown the diced bacon with the scallions & a little dash of cayenne for heat.
You can serve with crackers, but I prefer using lightly TOASTED sliced baguette, sesame loaf, or buttermilk biscuits.