When we read from 2/3 Torah scrolls is there a particular order they return to the Aaron Kodesh?

 

The proper order is that the Sefer Torah which was read last should be the first to be brought and put back in the Aaron kodesh.

However,  if the other Sefer Torah was taken first you should not rearrange who takes which Sefer, rather just put back the other Sefer Torah first.

 

Sources:

שערי אפרים שער י סעי’ מא