Preheat oven to 350°F.
Cut the jalapeños into a boat cut. (Click the link above to see how to do a Boat Cut.)
Place the jalapeños on a cookie sheet. Place sheet in preheated oven. Cook for about 20 - 30 minutes, until jalapeños are tender to the point that you like to eat them. (You will not be baking them further once you add the tuna, so make sure they are as done as you like now.)
Remove from oven and allow to cool slightly so you can handle them.
Turn oven to broil and allow to preheat.
Add cream cheese to each jalapeño to cover the bottom, leaving a concave "well" to place other ingredients. (Click the link above to see pictures of this step, if these instructions are unclear to you.)
Add a generous helping of the tuna salad.
Lay one or more slices of tomato on top of the tuna.
Place jalapeños back on cookie sheet.
Sprinkle or lay slices of Cheddar cheese over the top of all.
Place the cookie sheet back in the oven.
Broil, watching closely, just until cheese is hot and melted.
Remove from oven when done and enjoy.