When adding extra fruit to a muffin mix, should I alter the baking time or temperature.

If it were me,I would put them in a saucepan on low-medium heat and simmer them for a bit. This will thicken the liquid component. Then, I would use about 1/2 the amount and stir them into your muffin mix until barely combined. I might add a tablespoon or two of flour to the muffin mix. You can grind up the rest of the berries with a pinch of allspice and the zest of an orange & freeze it in a ziplock bag. (If you puree the berries, cooked or not, they make a good base for sauce for pork.)

Patrick - first, there's no rush from a food safety point of view to use up the whole berry cranberry sauce.
But if, yes, you want to use them now, you can
- whizz them in a smoothie
- layer with nuts or cereal in yogurt for a breakfast dish or snack
- heat up with some butter to make a sauce for pancakes or waffles
- even pour some over muffins baked according to a box or recipe

That is going to seriously alter the muffin mix, adding much more liquid to it than in the instructions. I think I’d consider doing something savory with that cranberry sauce instead.