I have a 2000 dakota that needs a heater core. How do I know which one. I see 2 different thickness and some people say they had to remove clips or something for the 2" one

 

Moving this to second gen dakota section for ya.

 

Both will work but the thicker one is better but to use the thicker one you will need to snap off 2 tabs in the HVAC housing or it will not fit they look like two prongs on the bottom of the housing you will see them as you remove the old core .

Your HVAC box may look different my Dakota is a 98 model.

BE EXTREAMLY CARELUF these parts are old plastic and will snap very easily especially the air vent flap clip I broke mine without much force I was lucky and had a second HVAC box as a spare.

Replacements do not exist on this planet