When making lemon/poppy seed icecream, how should I include the poppy seeds?
Poppy seeds have a very pleasant aroma and a bit of heat is going to do wonders to extract their flavour and aroma. I would dump them right into the end of the cooking process after you remove your custard from the heat. You don't want to cook them because you'll boil off volatiles and lose some flavour much like vanilla.
I think if you can get some lemon zest to appear in your finished product, or even as a garnish, along with the flecks of poppy it's going to look beautiful if you leave them in. Sort of a more sophisticated vanilla bean ice cream vibe.