I have a 88 with a C-4 trans. The trans lines got mixed up and I need to know which goes into which trans line hole on the radiator?

 

I dont think it matters but I would personlly think that the trans discharge should connect to the top of the radiator for gravity/less pumping reasons.
I just have mine run to a trans cooler only. Having it hooked to the radiator helps the trans heat up quicker & maintains that temperture. Depends on what you want or the trans needs for the type of conditions you indure.