it wouldnt effect it either way u put them on as they are both just inlets straight into the heater core...make sure u bleed it probly with the heater ON full
For easier pipe routing and to have the pipes spaced out, I went 2 to 3 and 1 to 4 on my swap. As you will find out by trial and error if you go 1 to 3 and 2 to 4 the heater hoses will be crossed and hitting each other.