If I am using a bivy sack
I use puffy clothing inside my bags rather than two layers. A benefit of that is less cooling from air movement against my body when I turn and much nicer when I get up for a pee.
If that does not work for you , putting the extra layer inside or outside would depend on a couple of things.
If you are using a down bag, go outside.(between the sb and the bivy)
It has been measured that up to about 50% compression down works just as well as non compressed.
(Richard Nisley, BPL)
(Some confuse the total compression under a body with partial compression...)
The reason for this is that you will have some dampness between the bag and the bivy so that would migrate to the synthetic layer on top rather then the fabric layer of your sb.
Now, if you are using a synthetic bag, inside would work better as long as it does not restrict your movements.