I see that the heater channel connects up near the motor, and since my car ha abit of rust and will need some work in the heter channel areas, do these need to be connected back up to the motor or can i just weld them up/block them off?

the ones on the motor and heater boxes on the exhaust just cover with some coke cans.
the ones under the back of car on the body, just put a spray can plasticcap over them.