I just bought and aftermarket radiator that has two unscrewable/removable nipples at the bottom which I'm guessing is for cooling oil or transmission fluid in an automatic transmission z. Is there any special way of capping these off so I can use the radiator in my manual transmission z?

 

It is its own closed system. You don't have to cap them off. No coolant or anything goes in/out. Its ATF that goes in and out of it.