However, I can't find instructions for freezing it. Should I cook it first? Should I leave it uncooked? Should I leave it uncooked, but cook the squash first?

This is the recipe that I was going to use:

http://www.bigoven.com/121601-Patty-Pan-Lasagna-recipe.html

I read you recipe and see no reason why you couldn't freeze it. I've never frozen squash but I freeze grated zucchini to bake with all the time.

I would cook it just as though you are going to have it for supper, but take it out before it is completely cooked, then cool and freeze.

I didn't look at the cooking time, but with regular lasagna I take it out 15 minutes early. That way it doesn't get over cooked when you reheat it. When I bring it up I let it thaw and put in the oven just until it's hot right through--usually about half an hour. If it starts to brown too much I cover it with tin foil