So I've purchased a fondant cake topper online, and it should arrive tomorrow.  I will order the cake today to be ready for Saturday.  At what point should the cake topper be put on, because I know at Walmart they refrigerate the cakes once done.  If they put the topper parts on and put it in the refrigerator, will that be ok?  Or should I just have them put it on when I pick it up?

It should be fine in the fridge.  But, you can put the topper on yourself.  Are you giving the topper to Walmart to put on your cake?  I wouldn't trust them with that.  Just put it on when you pick up the cake.