In what order do I place my troops in an APC?

This will depend on what you are doing but a good standard approach is to place fighters in the front as they have a short range of attack and good defense. Shooters go in the back row as there have long range of attack and put vehicles in the middle row.

There are various benefits though to using all the same type of troops in an APC formation especially when you are at a higher level and have unlocked war room buildings and have advanced your research.