I have finally put the heater core in and I am putting everything back together. I have two problems. I could not find where these 2 wire go to and I do not remember even removing them.
This one is behind the glove box and i had originally thought it went on the radio but it does not.
This second one is right under the steering wheel and I also do not remember removing it.
Any idea on what it connects to?

What year? Please provide vehicle info to your signature, it will help greatly when others are trying to help.

From the wiring diagrams for a 2005 Jeep CRD:
First Picture: Plug behind glove box looks like the "Blend Door" actuator connector
Wiring diagram in Factory Service Manual shows different wiring colors vs your picture, but it is a three plug connector and two of the wire colors match.
I could find no other 4 connector plugs with just 3 wires in it in that area.
*(3 wires: 1-Gray w/pink stripe wire, 1-Black wire, 1-Light Blue w/orange stripe wire

Second Picture: Plug looks to be the courtesy lamp connector that is on the kick panel under the steering wheel.
*(2 wires: 1-Red wire, 1-Black w/white stripe)

It’s a 2006. Does the blend door actuator go on the heater box?

You need to add that year to your signature.

The blend door actuator sets on top of the heater box.
Item NO. 24 on the diagram below.